Running as unit: rb-build-amd64_23-72371.service; invocation ID: afbdd92937584efd8df30e54bc6e8eb8 ==================================================================================== Thu Sep 18 05:15:03 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_23) on jenkins, called using "ionos11-amd64 ionos15-amd64" as arguments. Thu Sep 18 05:15:03 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-jEEVsi9x" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 05:15:03 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 05:15:03 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-00b6yz' Thu Sep 18 05:15:03 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Sep 18 05:15:03 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-aCNaeh' ok, let's check if staden-io-lib is building anywhere yet… ok, staden-io-lib is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of staden-io-lib in unstable on amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Thu Sep 18 05:15:10 UTC 2025 I: starting to build staden-io-lib/unstable/amd64 on jenkins on '2025-09-18 05:15' Thu Sep 18 05:15:10 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/72371/console.log 1758172510 amd64 unstable staden-io-lib Thu Sep 18 05:15:10 UTC 2025 I: Downloading source for unstable/staden-io-lib=1.15.0-1.1 --2025-09-18 05:15:11-- http://deb.debian.org/debian/pool/main/s/staden-io-lib/staden-io-lib_1.15.0-1.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2534 (2.5K) [text/prs.lines.tag] Saving to: ‘staden-io-lib_1.15.0-1.1.dsc’ 0K .. 100% 270M=0s 2025-09-18 05:15:11 (270 MB/s) - ‘staden-io-lib_1.15.0-1.1.dsc’ saved [2534/2534] --2025-09-18 05:15:11-- http://deb.debian.org/debian/pool/main/s/staden-io-lib/staden-io-lib_1.15.0-1.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2534 (2.5K) [text/prs.lines.tag] Saving to: ‘staden-io-lib_1.15.0-1.1.dsc’ 0K .. 100% 270M=0s 2025-09-18 05:15:11 (270 MB/s) - ‘staden-io-lib_1.15.0-1.1.dsc’ saved [2534/2534] Thu Sep 18 05:15:11 UTC 2025 I: staden-io-lib_1.15.0-1.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: staden-io-lib Binary: staden-io-lib-utils, libstaden-read-dev, libstaden-read14t64, staden-io-lib-examples Architecture: any all Version: 1.15.0-1.1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Thorsten Alteholz , Michael R. Crusoe Homepage: https://github.com/jkbonfield/io_lib Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/staden-io-lib Vcs-Git: https://salsa.debian.org/med-team/staden-io-lib.git Testsuite: autopkgtest Testsuite-Triggers: smalt-examples Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, libhtscodecs-dev, d-shlibs (>= 0.106), libbz2-dev, liblzma-dev Package-List: libstaden-read-dev deb libdevel optional arch=any libstaden-read14t64 deb libs optional arch=any staden-io-lib-examples deb science optional arch=all staden-io-lib-utils deb science optional arch=any Checksums-Sha1: fdb3fa8d3c5e27a05b45392e62dd5b9dc470dbc7 3381428 staden-io-lib_1.15.0.orig.tar.gz 1ae5fe311d3126a02ad8b2679246f7a7db5ab7c3 17208 staden-io-lib_1.15.0-1.1.debian.tar.xz Checksums-Sha256: 7006ab127ec05649d1f1bceafb7953defc665408da24cf990804d2c65e510f39 3381428 staden-io-lib_1.15.0.orig.tar.gz 9eb6ed4ad3f0494f2814f07b06026059ba4ea1afd24590ff29a6eccc11a17c27 17208 staden-io-lib_1.15.0-1.1.debian.tar.xz Files: d53896987c153de6ca1d639be0ece3f5 3381428 staden-io-lib_1.15.0.orig.tar.gz 8aae2d1a5f5459f7dfb4410df20fd81b 17208 staden-io-lib_1.15.0-1.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEpi0s+9ULm1vzYNVLFZ61xO/Id0wFAmXhzkQACgkQFZ61xO/I d0wVpA/+MeEP6xGtaAB8o6wEjGzs8fOu/MGMNwQ9KhB1UNFClE6lIXNE03jQ5CAl 59M+ob4BP1CkJHNN6ZDHMRucBHptPAoZpqAbmRIv6mfz7MdrBAeZuC3Gjhgym2eE 20j7wEsVHb7D7C7C2vRJqWM5MgaJZe4GcoZv6V4LXYcqI97021BbgoEEgmI/YKN0 C1g6lphbCzy6rfg3k4eG1MBeMHcMS+9V2x6syVDsy1RqsCar+O5lsG3WnjaYjjez F3qqVlOi7zPjkCw35/4Qh13R+wyc7c77uXqcEgrp09rGJzAKIx6qFuJ96pyAVvDM 8gYAJzzAkAPaDUF6EpRlgPxzYWUYYZIAtnuGA9Admb5Rpz6geZDWFmOrFUIXjdzL YfOZe7Oy5473GB3MITeqtqo8Mg26AA5zFmObbP8A9R+Chz9O13JRver9xoQuF+tP pLFswN31hWnU4T6CbH7whYHXlpY+PCqlI9BQS6N0ae1/97VLYeHPFyFBJq5mzFf+ BN1AOEFiZ7abkPo9xsrAEq1CFTtoXmActrr1zckGMSgmKKVt13Pmz7SOcOdqHaSL h2HXFFTM1OARfvPZ26Jngq+EuUVXx4FH5ddGqs7Ds18vZqJhOpDDBtdEakkIeqoG IZZcv1tSyJbO4goDuXYARjtj/MzYu3+up6RganvlVwZZOH+SYXg= =X5JW -----END PGP SIGNATURE----- Thu Sep 18 05:15:11 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 05:15:11 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu Sep 18 05:15:11 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu Sep 18 05:15:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 05:15:11 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-wWBlHy' ==================================================================================== Thu Sep 18 05:15:11 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 staden-io-lib unstable /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC 1.15.0-1.1" as arguments. Thu Sep 18 05:15:11 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-vataUU6l" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 05:15:11 UTC 2025 I: Downloading source for unstable/staden-io-lib=1.15.0-1.1 Reading package lists... NOTICE: 'staden-io-lib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/staden-io-lib.git Please use: git clone https://salsa.debian.org/med-team/staden-io-lib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3401 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (dsc) [2534 B] Get:2 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (tar) [3381 kB] Get:3 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (diff) [17.2 kB] Fetched 3401 kB in 0s (88.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'staden-io-lib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/staden-io-lib.git Please use: git clone https://salsa.debian.org/med-team/staden-io-lib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3401 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (dsc) [2534 B] Get:2 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (tar) [3381 kB] Get:3 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (diff) [17.2 kB] Fetched 3401 kB in 0s (88.1 MB/s) Download complete and in download only mode ============================================================================= Building staden-io-lib in unstable on amd64 on ionos11-amd64 now. Date: Thu Sep 18 05:15:11 UTC 2025 Date UTC: Thu Sep 18 05:15:11 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 17 17:15:12 -12 2025 I: pbuilder-time-stamp: 1758172512 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [staden-io-lib_1.15.0-1.1.dsc] I: copying [./staden-io-lib_1.15.0.orig.tar.gz] I: copying [./staden-io-lib_1.15.0-1.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./staden-io-lib_1.15.0-1.1.dsc: no acceptable signature found dpkg-source: info: extracting staden-io-lib in staden-io-lib-1.15.0 dpkg-source: info: unpacking staden-io-lib_1.15.0.orig.tar.gz dpkg-source: info: unpacking staden-io-lib_1.15.0-1.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pathmax.patch dpkg-source: info: applying fix_fseeko.patch dpkg-source: info: applying usedebianhtscodecs.patch dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1480077/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d756168538d94e1880fc38905fadc9ff' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1480077' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/pbuilderrc_B1pV --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b1 --logfile b1/build.log staden-io-lib_1.15.0-1.1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1480077/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, libhtscodecs-dev, d-shlibs (>= 0.106), libbz2-dev, liblzma-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-nss-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl4-nss-dev is not installed. pbuilder-satisfydepends-dummy depends on libhtscodecs-dev; however: Package libhtscodecs-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.106); however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtscodecs-dev{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.10-2 [458 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.10-2 [458 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.10-2 [1423 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.11.0-1 [101 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.15.1-1 [26.1 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.15.1-1 [196 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.3-1 [2979 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.16.0-1 [562 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Fetched 31.9 MB in 13s (2476 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. 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Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../15-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-3+b3_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../17-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../24-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../26-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../27-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../32-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:amd64. 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Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../39-libkdb5-10t64_1.21.3-5_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:amd64. Preparing to unpack .../40-libkadm5srv-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5srv-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:amd64. Preparing to unpack .../41-krb5-multidev_1.21.3-5_amd64.deb ... Unpacking krb5-multidev:amd64 (1.21.3-5) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../42-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../43-libbrotli-dev_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../44-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../45-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../46-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../47-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../48-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../49-libgnutls30t64_3.8.10-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../50-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../51-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../52-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../53-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../54-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../55-libngtcp2-16_1.15.1-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.15.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../56-libngtcp2-crypto-gnutls8_1.15.1-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../57-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../58-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../59-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../60-libcurl3t64-gnutls_8.16.0-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.16.0-1) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../61-libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:amd64. Preparing to unpack .../62-libunbound8_1.23.1-1_amd64.deb ... Unpacking libunbound8:amd64 (1.23.1-1) ... Selecting previously unselected package libgnutls-dane0t64:amd64. Preparing to unpack .../63-libgnutls-dane0t64_3.8.10-2_amd64.deb ... Unpacking libgnutls-dane0t64:amd64 (3.8.10-2) ... Selecting previously unselected package libgnutls-openssl27t64:amd64. Preparing to unpack .../64-libgnutls-openssl27t64_3.8.10-2_amd64.deb ... Unpacking libgnutls-openssl27t64:amd64 (3.8.10-2) ... Selecting previously unselected package libidn2-dev:amd64. Preparing to unpack .../65-libidn2-dev_2.3.8-4_amd64.deb ... Unpacking libidn2-dev:amd64 (2.3.8-4) ... Selecting previously unselected package libp11-kit-dev:amd64. Preparing to unpack .../66-libp11-kit-dev_0.25.5-3_amd64.deb ... Unpacking libp11-kit-dev:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:amd64. Preparing to unpack .../67-libtasn1-6-dev_4.20.0-2_amd64.deb ... Unpacking libtasn1-6-dev:amd64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../68-libgmpxx4ldbl_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../69-libgmp-dev_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package nettle-dev:amd64. Preparing to unpack .../70-nettle-dev_3.10.1-1_amd64.deb ... Unpacking nettle-dev:amd64 (3.10.1-1) ... Selecting previously unselected package libgnutls28-dev:amd64. Preparing to unpack .../71-libgnutls28-dev_3.8.10-2_amd64.deb ... Unpacking libgnutls28-dev:amd64 (3.8.10-2) ... Selecting previously unselected package libkrb5-dev:amd64. Preparing to unpack .../72-libkrb5-dev_1.21.3-5_amd64.deb ... Unpacking libkrb5-dev:amd64 (1.21.3-5) ... Selecting previously unselected package libldap-dev:amd64. Preparing to unpack .../73-libldap-dev_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap-dev:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../74-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../75-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../76-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:amd64. Preparing to unpack .../77-libnghttp2-dev_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-dev:amd64. Preparing to unpack .../78-libnghttp3-dev_1.11.0-1_amd64.deb ... 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Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up libhtscodecs-dev:amd64 (1.6.1-2) ... Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.23.1-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libssl-dev:amd64 (3.5.3-1) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up libnghttp3-dev:amd64 (1.11.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.15.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libngtcp2-dev:amd64 (1.15.1-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.10-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.10-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.16.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.15.1-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.16.0-1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/staden-io-lib-1.15.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../staden-io-lib_1.15.0-1.1_source.changes dpkg-buildpackage: info: source package staden-io-lib dpkg-buildpackage: info: source version 1.15.0-1.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Benjamin Drung dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_clean rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam rm -f config.sub config.guess ## ## Try to verify correct ABI version right in the beginning ## Strangely enough d-shlibmove fails in detecting it in this package ## Since upstream build system creates libstaden-read.so.11.1.0 this code is not ## activated but it should be considered in case of future problems with ABI version ## #UPSTREAMABI=`grep ^VERS_CURRENT configure.in | sed 's/^VERS_CURRENT[[:space:]]*=\([0-9]\+\)[[:space:]]*/\1/'` ; \ #DEBABI=`grep '^Package: libstaden-read[0-9]\+' debian/control | sed 's/Package: libstaden-read\([0-9]\+\)/\1/'` ; \ #if [ ${UPSTREAMABI} -ne ${DEBABI} ] ; then \ # echo "Upstream has bumped ABI to ${UPSTREAMABI} but Debian is using libstaden-read${DEBABI} (see bug #710225)" ; \ # exit 1 ; \ #fi make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:81: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:81: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:81: the top level configure.ac:101: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:101: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.ac:101: the top level configure.ac:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:102: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:156: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:156: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from... configure.ac:156: the top level configure.ac:157: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:157: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_zstd.m4:31: AX_ZSTD is expanded from... configure.ac:157: the top level configure.ac:190: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:190: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:190: the top level configure.ac:255: warning: AC_OUTPUT should be used without arguments. configure.ac:255: You should run autoupdate. configure.ac:79: installing './compile' configure.ac:81: installing './config.guess' configure.ac:81: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' io_lib/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' export ac_cv_func_mmap_fixed_mapped=yes && dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/x86_64-linux-gnu-ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 8.16.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking for zlib.h... yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for egrep... (cached) /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for stdio_ext.h... yes checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... yes checking for fileno... yes checking for fstat... yes checking for mallopt... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for declarations of fseeko and ftello... yes checking for getpagesize... yes checking for working mmap... (cached) yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... yes checking for fsync... yes checking that generated files are newer than configure... done === configuring in htscodecs (/build/reproducible-path/staden-io-lib-1.15.0/htscodecs) configure: WARNING: no configuration information is in htscodecs configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------- CONFIGURE SUMMARY -------------------------------------------------- Bzip2 enabled: yes lzma enabled: yes custom-buffering enabled: yes Using own crc: yes Libcurl enabled: yes Libdeflate enabled: no have libbsc: no Have zstd: no CC: gcc CFLAGS: -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection LDFLAGS: -Wl,-z,relro -Wl,-z,now LIBS: -lm -llzma -lbz2 make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_build -O--no-parallel make -j1 make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make all-recursive make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making all in io_lib make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -o libstaden_read_la-scf_extras.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -fPIC -DPIC -o .libs/libstaden_read_la-translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -fPIC -DPIC -o .libs/libstaden_read_la-fpoint.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -o libstaden_read_la-fpoint.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOABI.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -fPIC -DPIC -o .libs/libstaden_read_la-expFileIO.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -o libstaden_read_la-expFileIO.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOPlain.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-misc_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -o libstaden_read_la-misc_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-read_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -o libstaden_read_la-read_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c write_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-write_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c write_scf.c -o libstaden_read_la-write_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sff.c -fPIC -DPIC -o .libs/libstaden_read_la-sff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sff.c -o libstaden_read_la-sff.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c srf.c -fPIC -DPIC -o .libs/libstaden_read_la-srf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c srf.c -o libstaden_read_la-srf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-array.lo `test -f 'array.c' || echo './'`array.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c array.c -fPIC -DPIC -o .libs/libstaden_read_la-array.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c array.c -o libstaden_read_la-array.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compress.lo `test -f 'compress.c' || echo './'`compress.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compress.c -fPIC -DPIC -o .libs/libstaden_read_la-compress.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compress.c -o libstaden_read_la-compress.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -fPIC -DPIC -o .libs/libstaden_read_la-error.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -o libstaden_read_la-error.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -fPIC -DPIC -o .libs/libstaden_read_la-files.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -o libstaden_read_la-files.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -fPIC -DPIC -o .libs/libstaden_read_la-find.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -o libstaden_read_la-find.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mach-io.c -fPIC -DPIC -o .libs/libstaden_read_la-mach-io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mach-io.c -o libstaden_read_la-mach-io.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_trace_file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c open_trace_file.c -fPIC -DPIC -o .libs/libstaden_read_la-open_trace_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c open_trace_file.c -o libstaden_read_la-open_trace_file.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-read_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_alloc.c -o libstaden_read_la-read_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c strings.c -fPIC -DPIC -o .libs/libstaden_read_la-strings.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c strings.c -o libstaden_read_la-strings.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -fPIC -DPIC -o .libs/libstaden_read_la-traceType.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -fPIC -DPIC -o .libs/libstaden_read_la-xalloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -o libstaden_read_la-xalloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -fPIC -DPIC -o .libs/libstaden_read_la-vlen.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -fPIC -DPIC -o .libs/libstaden_read_la-hash_table.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -fPIC -DPIC -o .libs/libstaden_read_la-jenkins_lookup3.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 15:3:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/x86_64-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -llzma -lbz2 libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -lcurl -lhtscodecs -lm -llzma -lbz2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.3 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so") libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making all in progs make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o convert_trace.o convert_trace.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o makeSCF.o makeSCF.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o extract_seq.o extract_seq.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o extract_qual.o extract_qual.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection 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-ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o srf_filter.o srf_filter.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o srf_info.o srf_info.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_info srf_info.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o srf_list.o srf_list.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_list srf_list.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o hash_exp.o hash_exp.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_dump.o cram_dump.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_index.o cram_index.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scramble.o scramble.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_merge.o scram_merge.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_pileup.o scram_pileup.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_flagstat.o scram_flagstat.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_test.o scram_test.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_size.o cram_size.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_filter.o cram_filter.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making all in tests make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_io_test.o cram_io_test.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' echo "Do not run test suite for architecture independent builds" Do not run test suite for architecture independent builds make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_test -O--no-parallel -Nstaden-io-lib-examples make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making check in io_lib make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making check in progs make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making check in tests make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make check-TESTS make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' PASS: srf2fasta.test PASS: srf2fastq.test PASS: srf_info.test Reading archive ./data/both.srf. PASS: srf_filter.test NB: The next line is expected to be an error message Malformed or missing index hash. Consider running srf_index_hash Nbuckets = 16 Nused = 20 Avg chain = 1.250000 Chain var.= 0.812500 %age full = 81.250000 max len = 3 Chain 0 = 3 Chain 1 = 8 Chain 2 = 3 Chain 3 = 2 PASS: srf_index.test Loading ce.fa Generating ce#sorted.sam Generating ce#unsorted.sam === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram.test === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt30.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt31.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x longref.sam test.out/longref.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 -q test.out/longref.cram test.out/longref.sam ./compare_sam.pl test.out/longref.sam ./data/longref.sam PASS: scram_mt40.test PASS: cram_io.test === testing ./data/ce#5b_java.cram === ../progs/scramble -t4 -r ./data/ce.fa ./data/ce#5b_java.cram test.out/ce#5b_java.scramble.sam ./compare_sam.pl ./data/ce#5b_java.sam test.out/ce#5b_java.scramble.sam === testing ./data/tag_aux#aux_java.cram === ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#aux_java.cram test.out/tag_aux#aux_java.scramble.sam ./compare_sam.pl ./data/tag_aux#aux_java.sam test.out/tag_aux#aux_java.scramble.sam === testing ./data/xx#large_aux_java.cram === ../progs/scramble -t4 -r ./data/xx.fa ./data/xx#large_aux_java.cram test.out/xx#large_aux_java.scramble.sam ./compare_sam.pl ./data/xx#large_aux_java.sam test.out/xx#large_aux_java.scramble.sam === testing ./data/9827_rand3.cram === ../progs/scramble -t4 -r ./data/9827_rand3.cram ./data/9827_rand3.cram test.out/9827_rand3.scramble.sam ./data/9827_rand3.cram.fai: No such file or directory ./compare_sam.pl ./data/9827_rand3.sam test.out/9827_rand3.scramble.sam PASS: java.test =================== All 11 tests passed =================== make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel make -j1 install DESTDIR=/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making install in io_lib make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.3 /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.3 libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.3 libstaden-read.so.14; }; }) libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.3 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: chmod 644 /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: ranlib /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making install in progs make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/convert_trace /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/makeSCF /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_seq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_qual /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_fastq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_info /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_update /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/get_comment /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_tar /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_extract /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_list /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/trace_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_sff /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/append_sff /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/ztr_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_dump_all /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_index_hash /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_linear /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_hash /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fastq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fasta /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_filter /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_info /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_list /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_exp /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_index /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scramble /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_merge /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_pileup /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_flagstat /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_test /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_size /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_filter /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_filter make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making install in tests make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /usr/bin/install -c io_lib-config '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man1' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man3' /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man3' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man4' /usr/bin/install -c -m 644 man/man4/Read.4 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man4' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_install -a mkdir -p /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/bin mv /build/reproducible-path/staden-io-lib-1.15.0/debian/staden-io-lib-utils/usr/bin/io_lib-config /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/bin # # Call d-shlibmove to comply with library packaging guide d-shlibmove --commit \ --t64 \ --multiarch \ --devunversioned \ --exclude-la \ --movedev "debian/tmp/usr/include" usr \ --override s/libhtscodecs2-dev/libhtscodecs-dev/ \ debian/tmp/usr/lib/*/libstaden-read.so Library package automatic movement utility --> libbz2-dev package exists. --> libcurl4-gnutls-dev package exists. --> libhtscodecs-dev package exists. --> liblzma-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.3 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu PKGDEV=libstaden-read-dev PKGSHL=libstaden-read14t64 install -d -m 755 debian/libstaden-read-dev/usr mv debian/tmp/usr/include debian/libstaden-read-dev/usr mkdir -p /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/include/io_lib/ cp /build/reproducible-path/staden-io-lib-1.15.0/io_lib_config.h /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/include/io_lib/ # make sure io_lib-config --libs will not return -pie (see #825461) find debian/*/usr/bin -name io_lib-config -exec sed -i -e 's/ *-fPIE//' -e 's/ *-pie//' \{\} \; make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_install -i mkdir -p debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test # fix path to staden-io-lib executable in examples for tst in `ls tests/*.test` ; do \ sed -e 's#\.\./$top_builddir/progs/#/usr/bin/#' -e 's#$top_builddir/progs/#/usr/bin/#' ${tst} > debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/`basename ${tst}` ; \ done # remove autogenerated big data files rm -f debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/data/ce\#*sorted.sam make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_lintian -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_fixperms chmod +x debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.test debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.pl make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_fixperms -O--no-parallel -Nstaden-io-lib-examples dh_missing -O--no-parallel -Nstaden-io-lib-examples dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'staden-io-lib-utils' in '../staden-io-lib-utils_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'staden-io-lib-utils-dbgsym' in '../staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read-dev' in '../libstaden-read-dev_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read14t64' in '../libstaden-read14t64_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read14t64-dbgsym' in '../libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'staden-io-lib-examples' in '../staden-io-lib-examples_1.15.0-1.1_all.deb'. dpkg-genbuildinfo --build=binary -O../staden-io-lib_1.15.0-1.1_amd64.buildinfo dpkg-genchanges --build=binary -O../staden-io-lib_1.15.0-1.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1480077 and its subdirectories I: Current time: Wed Sep 17 17:27:52 -12 2025 I: pbuilder-time-stamp: 1758173272 Thu Sep 18 05:27:52 UTC 2025 I: Signing ./b1/staden-io-lib_1.15.0-1.1_amd64.buildinfo as staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc Thu Sep 18 05:27:52 UTC 2025 I: Signed ./b1/staden-io-lib_1.15.0-1.1_amd64.buildinfo as ./b1/staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc Thu Sep 18 05:27:52 UTC 2025 - build #1 for staden-io-lib/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 05:27:52 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-vataUU6l, removing. /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 05:27 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 05:15 b2 -rw------- 1 jenkins jenkins 3693 Sep 18 05:15 rbuildlog.H9KVtqR -rw-rw-r-- 1 jenkins jenkins 2534 Mar 1 2024 staden-io-lib_1.15.0-1.1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b1: total 4888 -rw-r--r-- 1 jenkins jenkins 447986 Sep 18 05:27 build.log -rw-r--r-- 1 jenkins jenkins 349800 Sep 18 05:27 libstaden-read-dev_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 575808 Sep 18 05:27 libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 270608 Sep 18 05:27 libstaden-read14t64_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2754072 Sep 18 05:27 staden-io-lib-examples_1.15.0-1.1_all.deb -rw-r--r-- 1 jenkins jenkins 362604 Sep 18 05:27 staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 171216 Sep 18 05:27 staden-io-lib-utils_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 17208 Sep 18 05:27 staden-io-lib_1.15.0-1.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2534 Sep 18 05:27 staden-io-lib_1.15.0-1.1.dsc -rw-r--r-- 1 jenkins jenkins 8532 Sep 18 05:27 staden-io-lib_1.15.0-1.1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9414 Sep 18 05:27 staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3122 Sep 18 05:27 staden-io-lib_1.15.0-1.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1356 Sep 18 05:27 staden-io-lib_1.15.0-1.1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b2: total 0 Thu Sep 18 05:27:53 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 17 17:15:12 -12 2025 I: pbuilder-time-stamp: 1758172512 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [staden-io-lib_1.15.0-1.1.dsc] I: copying [./staden-io-lib_1.15.0.orig.tar.gz] I: copying [./staden-io-lib_1.15.0-1.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./staden-io-lib_1.15.0-1.1.dsc: no acceptable signature found dpkg-source: info: extracting staden-io-lib in staden-io-lib-1.15.0 dpkg-source: info: unpacking staden-io-lib_1.15.0.orig.tar.gz dpkg-source: info: unpacking staden-io-lib_1.15.0-1.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pathmax.patch dpkg-source: info: applying fix_fseeko.patch dpkg-source: info: applying usedebianhtscodecs.patch dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1480077/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d756168538d94e1880fc38905fadc9ff' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1480077' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/pbuilderrc_B1pV --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b1 --logfile b1/build.log staden-io-lib_1.15.0-1.1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1480077/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, libhtscodecs-dev, d-shlibs (>= 0.106), libbz2-dev, liblzma-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-nss-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl4-nss-dev is not installed. pbuilder-satisfydepends-dummy depends on libhtscodecs-dev; however: Package libhtscodecs-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.106); however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtscodecs-dev{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.10-2 [458 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.10-2 [458 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.10-2 [1423 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.11.0-1 [101 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.15.1-1 [26.1 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.15.1-1 [196 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.3-1 [2979 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.16.0-1 [562 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Fetched 31.9 MB in 13s (2476 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../15-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-3+b3_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../17-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../24-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../26-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../27-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../32-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../33-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../34-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../35-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../36-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:amd64. Preparing to unpack .../37-libgssrpc4t64_1.21.3-5_amd64.deb ... Unpacking libgssrpc4t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:amd64. Preparing to unpack .../38-libkadm5clnt-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5clnt-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../39-libkdb5-10t64_1.21.3-5_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:amd64. Preparing to unpack .../40-libkadm5srv-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5srv-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:amd64. Preparing to unpack .../41-krb5-multidev_1.21.3-5_amd64.deb ... Unpacking krb5-multidev:amd64 (1.21.3-5) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../42-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../43-libbrotli-dev_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../44-libbz2-dev_1.0.8-6_amd64.deb ... 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Unpacking librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../84-libssl-dev_3.5.3-1_amd64.deb ... Unpacking libssl-dev:amd64 (3.5.3-1) ... Selecting previously unselected package libssh2-1-dev:amd64. Preparing to unpack .../85-libssh2-1-dev_1.11.1-1_amd64.deb ... Unpacking libssh2-1-dev:amd64 (1.11.1-1) ... Selecting previously unselected package libzstd-dev:amd64. Preparing to unpack .../86-libzstd-dev_1.5.7+dfsg-1.1_amd64.deb ... Unpacking libzstd-dev:amd64 (1.5.7+dfsg-1.1) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../87-libcurl4-gnutls-dev_8.16.0-1_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (8.16.0-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../88-libhtscodecs2_1.6.1-2_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.1-2) ... Selecting previously unselected package libhtscodecs-dev:amd64. 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Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up libhtscodecs-dev:amd64 (1.6.1-2) ... Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.23.1-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libssl-dev:amd64 (3.5.3-1) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up libnghttp3-dev:amd64 (1.11.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.15.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libngtcp2-dev:amd64 (1.15.1-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.10-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.10-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.16.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.15.1-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.16.0-1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/staden-io-lib-1.15.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../staden-io-lib_1.15.0-1.1_source.changes dpkg-buildpackage: info: source package staden-io-lib dpkg-buildpackage: info: source version 1.15.0-1.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Benjamin Drung dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_clean rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam rm -f config.sub config.guess ## ## Try to verify correct ABI version right in the beginning ## Strangely enough d-shlibmove fails in detecting it in this package ## Since upstream build system creates libstaden-read.so.11.1.0 this code is not ## activated but it should be considered in case of future problems with ABI version ## #UPSTREAMABI=`grep ^VERS_CURRENT configure.in | sed 's/^VERS_CURRENT[[:space:]]*=\([0-9]\+\)[[:space:]]*/\1/'` ; \ #DEBABI=`grep '^Package: libstaden-read[0-9]\+' debian/control | sed 's/Package: libstaden-read\([0-9]\+\)/\1/'` ; \ #if [ ${UPSTREAMABI} -ne ${DEBABI} ] ; then \ # echo "Upstream has bumped ABI to ${UPSTREAMABI} but Debian is using libstaden-read${DEBABI} (see bug #710225)" ; \ # exit 1 ; \ #fi make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:81: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:81: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:81: the top level configure.ac:101: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:101: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.ac:101: the top level configure.ac:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:102: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:156: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:156: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from... configure.ac:156: the top level configure.ac:157: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:157: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_zstd.m4:31: AX_ZSTD is expanded from... configure.ac:157: the top level configure.ac:190: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:190: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:190: the top level configure.ac:255: warning: AC_OUTPUT should be used without arguments. configure.ac:255: You should run autoupdate. configure.ac:79: installing './compile' configure.ac:81: installing './config.guess' configure.ac:81: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' io_lib/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' export ac_cv_func_mmap_fixed_mapped=yes && dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/x86_64-linux-gnu-ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 8.16.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking for zlib.h... yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for egrep... (cached) /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for stdio_ext.h... yes checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... yes checking for fileno... yes checking for fstat... yes checking for mallopt... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for declarations of fseeko and ftello... yes checking for getpagesize... yes checking for working mmap... (cached) yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... yes checking for fsync... yes checking that generated files are newer than configure... done === configuring in htscodecs (/build/reproducible-path/staden-io-lib-1.15.0/htscodecs) configure: WARNING: no configuration information is in htscodecs configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------- CONFIGURE SUMMARY -------------------------------------------------- Bzip2 enabled: yes lzma enabled: yes custom-buffering enabled: yes Using own crc: yes Libcurl enabled: yes Libdeflate enabled: no have libbsc: no Have zstd: no CC: gcc CFLAGS: -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection LDFLAGS: -Wl,-z,relro -Wl,-z,now LIBS: -lm -llzma -lbz2 make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_build -O--no-parallel make -j1 make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make all-recursive make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making all in io_lib make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -o libstaden_read_la-scf_extras.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -fPIC -DPIC -o .libs/libstaden_read_la-translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -fPIC -DPIC -o .libs/libstaden_read_la-fpoint.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -o libstaden_read_la-fpoint.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOABI.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -fPIC -DPIC -o .libs/libstaden_read_la-expFileIO.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -o libstaden_read_la-expFileIO.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOPlain.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-misc_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -o libstaden_read_la-misc_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-read_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -o libstaden_read_la-read_scf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c write_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-write_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 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-Werror=format-security -fcf-protection -c sff.c -fPIC -DPIC -o .libs/libstaden_read_la-sff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sff.c -o libstaden_read_la-sff.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c srf.c -fPIC -DPIC -o .libs/libstaden_read_la-srf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c srf.c -o libstaden_read_la-srf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-array.lo `test -f 'array.c' || echo './'`array.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c array.c -fPIC -DPIC -o .libs/libstaden_read_la-array.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c array.c -o libstaden_read_la-array.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compress.lo `test -f 'compress.c' || echo './'`compress.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compress.c -fPIC -DPIC -o .libs/libstaden_read_la-compress.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compress.c -o libstaden_read_la-compress.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -fPIC -DPIC -o .libs/libstaden_read_la-error.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -o libstaden_read_la-error.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -fPIC -DPIC -o .libs/libstaden_read_la-files.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -o libstaden_read_la-files.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -fPIC -DPIC -o .libs/libstaden_read_la-find.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -o libstaden_read_la-find.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mach-io.c -fPIC -DPIC -o .libs/libstaden_read_la-mach-io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mach-io.c -o libstaden_read_la-mach-io.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_trace_file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c open_trace_file.c -fPIC -DPIC -o .libs/libstaden_read_la-open_trace_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c open_trace_file.c -o libstaden_read_la-open_trace_file.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-read_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_alloc.c -o libstaden_read_la-read_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c strings.c -fPIC -DPIC -o .libs/libstaden_read_la-strings.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c strings.c -o libstaden_read_la-strings.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -fPIC -DPIC -o .libs/libstaden_read_la-traceType.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -fPIC -DPIC -o .libs/libstaden_read_la-xalloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -o libstaden_read_la-xalloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -fPIC -DPIC -o .libs/libstaden_read_la-vlen.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -fPIC -DPIC -o .libs/libstaden_read_la-hash_table.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -fPIC -DPIC -o .libs/libstaden_read_la-jenkins_lookup3.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 15:3:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/x86_64-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -llzma -lbz2 libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -lcurl -lhtscodecs -lm -llzma -lbz2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.3 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so") libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making all in progs make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o convert_trace.o convert_trace.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration 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../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_size.o cram_size.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_filter.o cram_filter.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making all in tests make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_io_test.o cram_io_test.c /bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' echo "Do not run test suite for architecture independent builds" Do not run test suite for architecture independent builds make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_test -O--no-parallel -Nstaden-io-lib-examples make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making check in io_lib make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making check in progs make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making check in tests make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make check-TESTS make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' PASS: srf2fasta.test PASS: srf2fastq.test PASS: srf_info.test Reading archive ./data/both.srf. PASS: srf_filter.test NB: The next line is expected to be an error message Malformed or missing index hash. Consider running srf_index_hash Nbuckets = 16 Nused = 20 Avg chain = 1.250000 Chain var.= 0.812500 %age full = 81.250000 max len = 3 Chain 0 = 3 Chain 1 = 8 Chain 2 = 3 Chain 3 = 2 PASS: srf_index.test Loading ce.fa Generating ce#sorted.sam Generating ce#unsorted.sam === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram.test === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt30.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt31.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x longref.sam test.out/longref.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 -q test.out/longref.cram test.out/longref.sam ./compare_sam.pl test.out/longref.sam ./data/longref.sam PASS: scram_mt40.test PASS: cram_io.test === testing ./data/ce#5b_java.cram === ../progs/scramble -t4 -r ./data/ce.fa ./data/ce#5b_java.cram test.out/ce#5b_java.scramble.sam ./compare_sam.pl ./data/ce#5b_java.sam test.out/ce#5b_java.scramble.sam === testing ./data/tag_aux#aux_java.cram === ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#aux_java.cram test.out/tag_aux#aux_java.scramble.sam ./compare_sam.pl ./data/tag_aux#aux_java.sam test.out/tag_aux#aux_java.scramble.sam === testing ./data/xx#large_aux_java.cram === ../progs/scramble -t4 -r ./data/xx.fa ./data/xx#large_aux_java.cram test.out/xx#large_aux_java.scramble.sam ./compare_sam.pl ./data/xx#large_aux_java.sam test.out/xx#large_aux_java.scramble.sam === testing ./data/9827_rand3.cram === ../progs/scramble -t4 -r ./data/9827_rand3.cram ./data/9827_rand3.cram test.out/9827_rand3.scramble.sam ./data/9827_rand3.cram.fai: No such file or directory ./compare_sam.pl ./data/9827_rand3.sam test.out/9827_rand3.scramble.sam PASS: java.test =================== All 11 tests passed =================== make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel make -j1 install DESTDIR=/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making install in io_lib make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.3 /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.3 libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.3 libstaden-read.so.14; }; }) libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.3 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: chmod 644 /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: ranlib /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making install in progs make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/convert_trace /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/makeSCF /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_seq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_qual /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_fastq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_info /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_update /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/get_comment /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_tar /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_extract /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_list /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/trace_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_sff /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/append_sff /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/ztr_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_dump_all /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_index_hash /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_linear /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_hash /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fastq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fasta /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_filter /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_info /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_list /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_exp /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_index /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scramble /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_merge /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_pileup /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_flagstat /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_test /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_size /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_filter /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_filter make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making install in tests make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /usr/bin/install -c io_lib-config '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man1' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man3' /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man3' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man4' /usr/bin/install -c -m 644 man/man4/Read.4 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man4' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_install -a mkdir -p /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/bin mv /build/reproducible-path/staden-io-lib-1.15.0/debian/staden-io-lib-utils/usr/bin/io_lib-config /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/bin # # Call d-shlibmove to comply with library packaging guide d-shlibmove --commit \ --t64 \ --multiarch \ --devunversioned \ --exclude-la \ --movedev "debian/tmp/usr/include" usr \ --override s/libhtscodecs2-dev/libhtscodecs-dev/ \ debian/tmp/usr/lib/*/libstaden-read.so Library package automatic movement utility --> libbz2-dev package exists. --> libcurl4-gnutls-dev package exists. --> libhtscodecs-dev package exists. --> liblzma-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.3 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu PKGDEV=libstaden-read-dev PKGSHL=libstaden-read14t64 install -d -m 755 debian/libstaden-read-dev/usr mv debian/tmp/usr/include debian/libstaden-read-dev/usr mkdir -p /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/include/io_lib/ cp /build/reproducible-path/staden-io-lib-1.15.0/io_lib_config.h /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/include/io_lib/ # make sure io_lib-config --libs will not return -pie (see #825461) find debian/*/usr/bin -name io_lib-config -exec sed -i -e 's/ *-fPIE//' -e 's/ *-pie//' \{\} \; make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_install -i mkdir -p debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test # fix path to staden-io-lib executable in examples for tst in `ls tests/*.test` ; do \ sed -e 's#\.\./$top_builddir/progs/#/usr/bin/#' -e 's#$top_builddir/progs/#/usr/bin/#' ${tst} > debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/`basename ${tst}` ; \ done # remove autogenerated big data files rm -f debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/data/ce\#*sorted.sam make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_lintian -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_fixperms chmod +x debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.test debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.pl make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_fixperms -O--no-parallel -Nstaden-io-lib-examples dh_missing -O--no-parallel -Nstaden-io-lib-examples dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'staden-io-lib-utils' in '../staden-io-lib-utils_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'staden-io-lib-utils-dbgsym' in '../staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read-dev' in '../libstaden-read-dev_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read14t64' in '../libstaden-read14t64_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read14t64-dbgsym' in '../libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'staden-io-lib-examples' in '../staden-io-lib-examples_1.15.0-1.1_all.deb'. dpkg-genbuildinfo --build=binary -O../staden-io-lib_1.15.0-1.1_amd64.buildinfo dpkg-genchanges --build=binary -O../staden-io-lib_1.15.0-1.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1480077 and its subdirectories I: Current time: Wed Sep 17 17:27:52 -12 2025 I: pbuilder-time-stamp: 1758173272 Thu Sep 18 05:27:53 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Sep 18 05:27:53 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Sep 18 05:27:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Sep 18 05:27:53 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-i2KLkL' ==================================================================================== Wed Oct 21 11:50:53 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 staden-io-lib unstable /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC 1.15.0-1.1" as arguments. Wed Oct 21 11:50:53 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-EVOt7yVo" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Oct 21 11:50:53 UTC 2026 I: Downloading source for unstable/staden-io-lib=1.15.0-1.1 Reading package lists... NOTICE: 'staden-io-lib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/staden-io-lib.git Please use: git clone https://salsa.debian.org/med-team/staden-io-lib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3401 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (dsc) [2534 B] Get:2 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (tar) [3381 kB] Get:3 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (diff) [17.2 kB] Fetched 3401 kB in 0s (69.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'staden-io-lib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/staden-io-lib.git Please use: git clone https://salsa.debian.org/med-team/staden-io-lib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3401 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (dsc) [2534 B] Get:2 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (tar) [3381 kB] Get:3 http://deb.debian.org/debian unstable/main staden-io-lib 1.15.0-1.1 (diff) [17.2 kB] Fetched 3401 kB in 0s (69.5 MB/s) Download complete and in download only mode ============================================================================= Re-Building staden-io-lib in unstable on amd64 on ionos15-amd64 now. Date: Wed Oct 21 11:50:54 UTC 2026 Date UTC: Wed Oct 21 11:50:54 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/pbuilderrc_TMiw + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' staden-io-lib = debian-installer -o staden-io-lib = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' staden-io-lib = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/pbuilderrc_TMiw --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b2 --logfile b2/build.log staden-io-lib_1.15.0-1.1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 22 01:50:54 +14 2026 I: pbuilder-time-stamp: 1792583454 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [staden-io-lib_1.15.0-1.1.dsc] I: copying [./staden-io-lib_1.15.0.orig.tar.gz] I: copying [./staden-io-lib_1.15.0-1.1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./staden-io-lib_1.15.0-1.1.dsc: no acceptable signature found dpkg-source: info: extracting staden-io-lib in staden-io-lib-1.15.0 dpkg-source: info: unpacking staden-io-lib_1.15.0.orig.tar.gz dpkg-source: info: unpacking staden-io-lib_1.15.0-1.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pathmax.patch dpkg-source: info: applying fix_fseeko.patch dpkg-source: info: applying usedebianhtscodecs.patch dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 21 11:51 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=75a94e6b188e4d0bb5aea7e798930642 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3176574 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/pbuilderrc_TMiw --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b2 --logfile b2/build.log staden-io-lib_1.15.0-1.1.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, libhtscodecs-dev, d-shlibs (>= 0.106), libbz2-dev, liblzma-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-nss-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl4-nss-dev is not installed. pbuilder-satisfydepends-dummy depends on libhtscodecs-dev; however: Package libhtscodecs-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.106); however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtscodecs-dev{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 31.9 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-1 [431 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.10-2 [458 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.10-2 [458 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.10-2 [1423 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.11.0-1 [101 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.15.1-1 [26.1 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.15.1-1 [196 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.3-1 [2979 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.16.0-1 [562 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Fetched 31.9 MB in 8s (3801 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. 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Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.15.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libngtcp2-dev:amd64 (1.15.1-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.10-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.10-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.16.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.15.1-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.16.0-1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/staden-io-lib-1.15.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../staden-io-lib_1.15.0-1.1_source.changes dpkg-buildpackage: info: source package staden-io-lib dpkg-buildpackage: info: source version 1.15.0-1.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Benjamin Drung dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_clean rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam rm -f config.sub config.guess ## ## Try to verify correct ABI version right in the beginning ## Strangely enough d-shlibmove fails in detecting it in this package ## Since upstream build system creates libstaden-read.so.11.1.0 this code is not ## activated but it should be considered in case of future problems with ABI version ## #UPSTREAMABI=`grep ^VERS_CURRENT configure.in | sed 's/^VERS_CURRENT[[:space:]]*=\([0-9]\+\)[[:space:]]*/\1/'` ; \ #DEBABI=`grep '^Package: libstaden-read[0-9]\+' debian/control | sed 's/Package: libstaden-read\([0-9]\+\)/\1/'` ; \ #if [ ${UPSTREAMABI} -ne ${DEBABI} ] ; then \ # echo "Upstream has bumped ABI to ${UPSTREAMABI} but Debian is using libstaden-read${DEBABI} (see bug #710225)" ; \ # exit 1 ; \ #fi make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:81: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:81: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:81: the top level configure.ac:101: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:101: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from... configure.ac:101: the top level configure.ac:102: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:102: warning: The macro 'AC_LANG_C' is obsolete. configure.ac:102: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from... configure.ac:102: the top level configure.ac:156: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:156: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from... configure.ac:156: the top level configure.ac:157: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:157: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... m4/ax_with_zstd.m4:31: AX_ZSTD is expanded from... configure.ac:157: the top level configure.ac:190: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:190: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:190: the top level configure.ac:255: warning: AC_OUTPUT should be used without arguments. configure.ac:255: You should run autoupdate. configure.ac:79: installing './compile' configure.ac:81: installing './config.guess' configure.ac:81: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' io_lib/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' export ac_cv_func_mmap_fixed_mapped=yes && dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/x86_64-linux-gnu-ld checking if the linker (/usr/bin/x86_64-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/x86_64-linux-gnu-ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/x86_64-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 8.16.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking for zlib.h... yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for egrep... (cached) /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for fcntl.h... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking for stdio_ext.h... yes checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... yes checking for fileno... yes checking for fstat... yes checking for mallopt... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for declarations of fseeko and ftello... yes checking for getpagesize... yes checking for working mmap... (cached) yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... yes checking for fsync... yes checking that generated files are newer than configure... done === configuring in htscodecs (/build/reproducible-path/staden-io-lib-1.15.0/htscodecs) configure: WARNING: no configuration information is in htscodecs configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib/version.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------- CONFIGURE SUMMARY -------------------------------------------------- Bzip2 enabled: yes lzma enabled: yes custom-buffering enabled: yes Using own crc: yes Libcurl enabled: yes Libdeflate enabled: no have libbsc: no Have zstd: no CC: gcc CFLAGS: -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection LDFLAGS: -Wl,-z,relro -Wl,-z,now LIBS: -lm -llzma -lbz2 make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_build -O--no-parallel make -j1 make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make all-recursive make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making all in io_lib make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -o libstaden_read_la-scf_extras.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -fPIC -DPIC -o .libs/libstaden_read_la-translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -fPIC -DPIC -o .libs/libstaden_read_la-fpoint.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -o libstaden_read_la-fpoint.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOABI.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -fPIC -DPIC -o .libs/libstaden_read_la-expFileIO.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -o libstaden_read_la-expFileIO.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOPlain.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-misc_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -o libstaden_read_la-misc_scf.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-read_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -o libstaden_read_la-read_scf.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c write_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-write_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c write_scf.c -o libstaden_read_la-write_scf.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sff.c -fPIC -DPIC -o .libs/libstaden_read_la-sff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sff.c -o libstaden_read_la-sff.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c srf.c -fPIC -DPIC -o .libs/libstaden_read_la-srf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c srf.c -o libstaden_read_la-srf.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-array.lo `test -f 'array.c' || echo './'`array.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c array.c -fPIC -DPIC -o .libs/libstaden_read_la-array.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c array.c -o libstaden_read_la-array.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compress.lo `test -f 'compress.c' || echo './'`compress.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compress.c -fPIC -DPIC -o .libs/libstaden_read_la-compress.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compress.c -o libstaden_read_la-compress.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -fPIC -DPIC -o .libs/libstaden_read_la-error.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -o libstaden_read_la-error.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -fPIC -DPIC -o .libs/libstaden_read_la-files.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -o libstaden_read_la-files.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -fPIC -DPIC -o .libs/libstaden_read_la-find.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -o libstaden_read_la-find.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mach-io.c -fPIC -DPIC -o .libs/libstaden_read_la-mach-io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mach-io.c -o libstaden_read_la-mach-io.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_trace_file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c open_trace_file.c -fPIC -DPIC -o .libs/libstaden_read_la-open_trace_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c open_trace_file.c -o libstaden_read_la-open_trace_file.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-read_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_alloc.c -o libstaden_read_la-read_alloc.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c strings.c -fPIC -DPIC -o .libs/libstaden_read_la-strings.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c strings.c -o libstaden_read_la-strings.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -fPIC -DPIC -o .libs/libstaden_read_la-traceType.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -fPIC -DPIC -o .libs/libstaden_read_la-xalloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -o libstaden_read_la-xalloc.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -fPIC -DPIC -o .libs/libstaden_read_la-vlen.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -fPIC -DPIC -o .libs/libstaden_read_la-hash_table.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -fPIC -DPIC -o .libs/libstaden_read_la-jenkins_lookup3.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 15:3:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/x86_64-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo 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libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -llzma -lbz2 libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -lcurl -lhtscodecs -lm -llzma -lbz2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.3 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so") libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making all in progs make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o convert_trace.o convert_trace.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o makeSCF.o makeSCF.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o extract_seq.o extract_seq.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o extract_qual.o extract_qual.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o extract_fastq.o extract_fastq.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_fastq extract_fastq.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o index_tar.o index_tar.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o index_tar index_tar.o -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o index_tar index_tar.o -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scf_dump.o scf_dump.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scf_dump scf_dump.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scf_info.o scf_info.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scf_info scf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scf_info scf_info.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. 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srf_list.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_list srf_list.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o hash_exp.o hash_exp.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_dump.o cram_dump.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_index.o cram_index.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scramble.o scramble.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_merge.o scram_merge.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_pileup.o scram_pileup.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_flagstat.o scram_flagstat.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_test.o scram_test.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_size.o cram_size.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_filter.o cram_filter.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making all in tests make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_io_test.o cram_io_test.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' echo "Do not run test suite for architecture independent builds" Do not run test suite for architecture independent builds make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_auto_test -O--no-parallel -Nstaden-io-lib-examples make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making check in io_lib make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making check in progs make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making check in tests make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make check-TESTS make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' PASS: srf2fasta.test PASS: srf2fastq.test PASS: srf_info.test Reading archive ./data/both.srf. PASS: srf_filter.test NB: The next line is expected to be an error message Malformed or missing index hash. Consider running srf_index_hash Nbuckets = 16 Nused = 20 Avg chain = 1.250000 Chain var.= 0.812500 %age full = 81.250000 max len = 3 Chain 0 = 3 Chain 1 = 8 Chain 2 = 3 Chain 3 = 2 PASS: srf_index.test Loading ce.fa Generating ce#sorted.sam Generating ce#unsorted.sam === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram.test === testing ./data/c1#bounds.sam === ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -V3.0 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -V3.0 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -V3.0 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt30.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V3.1 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam PASS: scram_mt31.test === testing ./data/c1#bounds.sam === ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam === testing ./data/c1#clip.sam === ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam === testing ./data/c1#pad1.sam === ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam === testing ./data/c1#pad2.sam === ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam === testing ./data/c1#pad3.sam === ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam === testing ./data/ce#1.sam === ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam === testing ./data/ce#2.sam === ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam === testing ./data/ce#5.sam === ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam === testing ./data/ce#5b.sam === ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam === testing ./data/ce#large_seq.sam === ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam === testing ./data/ce#sorted.sam === ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam === testing ./data/ce#tag_depadded.sam === ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam === testing ./data/ce#tag_padded.sam === ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam === testing ./data/ce#unmap.sam === ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam === testing ./data/ce#unmap1.sam === ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam === testing ./data/ce#unmap2.sam === ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam === testing ./data/ce#unsorted.sam === ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam === testing ./data/tag_aux#aux.sam === ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam === testing ./data/tag_aux#special.sam === ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam === testing ./data/tag_aux#values1.bam === ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam === testing ./data/tag_aux#values2.bam === ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam === testing ./data/tag_aux#values4.bam === ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam ../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded reference with non-coordinate sorted data is not supported. Using -x for no-ref instead. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Embedded consensus with non-coordinate sorted data is not supported. ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam === testing ./data/xx#MD.sam === ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam === testing ./data/xx#MD2.sam === ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam === testing ./data/xx#blank.sam === ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam === testing ./data/xx#large_aux.sam === ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam === testing ./data/xx#large_aux2.sam === ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam === testing ./data/xx#minimal.sam === ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam === testing ./data/xx#pair.sam === ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam === testing ./data/xx#repeated.sam === ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam === testing ./data/xx#rg.sam === ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam === testing ./data/xx#triplet.sam === ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam === testing ./data/xx#unsorted.sam === ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam ../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam ../progs/scramble -t4 -V4.0 -7 -x longref.sam test.out/longref.cram WARNING: this version of CRAM is not a recognised GA4GH standard. Note this CRAM version is a technology demonstration only. Future versions of Scramble may not be able to read these files. Unsorted mode enabled ../progs/scramble -t4 -q test.out/longref.cram test.out/longref.sam ./compare_sam.pl test.out/longref.sam ./data/longref.sam PASS: scram_mt40.test PASS: cram_io.test === testing ./data/ce#5b_java.cram === ../progs/scramble -t4 -r ./data/ce.fa ./data/ce#5b_java.cram test.out/ce#5b_java.scramble.sam ./compare_sam.pl ./data/ce#5b_java.sam test.out/ce#5b_java.scramble.sam === testing ./data/tag_aux#aux_java.cram === ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#aux_java.cram test.out/tag_aux#aux_java.scramble.sam ./compare_sam.pl ./data/tag_aux#aux_java.sam test.out/tag_aux#aux_java.scramble.sam === testing ./data/xx#large_aux_java.cram === ../progs/scramble -t4 -r ./data/xx.fa ./data/xx#large_aux_java.cram test.out/xx#large_aux_java.scramble.sam ./compare_sam.pl ./data/xx#large_aux_java.sam test.out/xx#large_aux_java.scramble.sam === testing ./data/9827_rand3.cram === ../progs/scramble -t4 -r ./data/9827_rand3.cram ./data/9827_rand3.cram test.out/9827_rand3.scramble.sam ./data/9827_rand3.cram.fai: No such file or directory ./compare_sam.pl ./data/9827_rand3.sam test.out/9827_rand3.scramble.sam PASS: java.test =================== All 11 tests passed =================== make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install -O--no-parallel make -j1 install DESTDIR=/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making install in io_lib make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.3 /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.3 libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.3 libstaden-read.so.14; }; }) libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.3 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: chmod 644 /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: install: ranlib /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' Making install in progs make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/convert_trace /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/makeSCF /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_seq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_qual /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_fastq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_info /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_update /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/get_comment /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_tar /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_extract /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_list /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/trace_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_sff /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/append_sff /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/ztr_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_dump_all /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_index_hash /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_linear /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_hash /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fastq /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fasta /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_filter /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_info /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_list /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_exp /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_dump /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_index /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scramble /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_merge /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_pileup /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_flagstat /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_test /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_size /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_filter /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/cram_filter make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making install in tests make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /usr/bin/install -c io_lib-config '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man1' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man3' /usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man3' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man4' /usr/bin/install -c -m 644 man/man4/Read.4 '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/share/man/man4' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' /usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/include/io_lib' make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[2]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_install -a mkdir -p /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/bin mv /build/reproducible-path/staden-io-lib-1.15.0/debian/staden-io-lib-utils/usr/bin/io_lib-config /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/bin # # Call d-shlibmove to comply with library packaging guide d-shlibmove --commit \ --t64 \ --multiarch \ --devunversioned \ --exclude-la \ --movedev "debian/tmp/usr/include" usr \ --override s/libhtscodecs2-dev/libhtscodecs-dev/ \ debian/tmp/usr/lib/*/libstaden-read.so Library package automatic movement utility --> libbz2-dev package exists. --> libcurl4-gnutls-dev package exists. --> libhtscodecs-dev package exists. --> liblzma-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.3 debian/libstaden-read14t64/usr/lib/x86_64-linux-gnu PKGDEV=libstaden-read-dev PKGSHL=libstaden-read14t64 install -d -m 755 debian/libstaden-read-dev/usr mv debian/tmp/usr/include debian/libstaden-read-dev/usr mkdir -p /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/include/io_lib/ cp /build/reproducible-path/staden-io-lib-1.15.0/io_lib_config.h /build/reproducible-path/staden-io-lib-1.15.0/debian/libstaden-read-dev/usr/include/io_lib/ # make sure io_lib-config --libs will not return -pie (see #825461) find debian/*/usr/bin -name io_lib-config -exec sed -i -e 's/ *-fPIE//' -e 's/ *-pie//' \{\} \; make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_install -i mkdir -p debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test # fix path to staden-io-lib executable in examples for tst in `ls tests/*.test` ; do \ sed -e 's#\.\./$top_builddir/progs/#/usr/bin/#' -e 's#$top_builddir/progs/#/usr/bin/#' ${tst} > debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/`basename ${tst}` ; \ done # remove autogenerated big data files rm -f debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/data/ce\#*sorted.sam make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_lintian -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_fixperms chmod +x debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.test debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.pl make[1]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0' dh_fixperms -O--no-parallel -Nstaden-io-lib-examples dh_missing -O--no-parallel -Nstaden-io-lib-examples dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'staden-io-lib-utils' in '../staden-io-lib-utils_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'staden-io-lib-utils-dbgsym' in '../staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read-dev' in '../libstaden-read-dev_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read14t64' in '../libstaden-read14t64_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'libstaden-read14t64-dbgsym' in '../libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb'. dpkg-deb: building package 'staden-io-lib-examples' in '../staden-io-lib-examples_1.15.0-1.1_all.deb'. dpkg-genbuildinfo --build=binary -O../staden-io-lib_1.15.0-1.1_amd64.buildinfo dpkg-genchanges --build=binary -O../staden-io-lib_1.15.0-1.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3176574 and its subdirectories I: Current time: Thu Oct 22 02:07:33 +14 2026 I: pbuilder-time-stamp: 1792584453 + false + set +x Wed Oct 21 12:07:33 UTC 2026 I: Signing ./b2/staden-io-lib_1.15.0-1.1_amd64.buildinfo as staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc Wed Oct 21 12:07:33 UTC 2026 I: Signed ./b2/staden-io-lib_1.15.0-1.1_amd64.buildinfo as ./b2/staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc Wed Oct 21 12:07:33 UTC 2026 - build #2 for staden-io-lib/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed Oct 21 12:07:33 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-EVOt7yVo, removing. /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC: total 460 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 05:27 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 05:44 b2 -rw------- 1 jenkins jenkins 451968 Sep 18 05:27 rbuildlog.H9KVtqR -rw-rw-r-- 1 jenkins jenkins 2534 Mar 1 2024 staden-io-lib_1.15.0-1.1.dsc /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b1: total 4916 -rw-r--r-- 1 jenkins jenkins 447986 Sep 18 05:27 build.log -rw-r--r-- 1 jenkins jenkins 349800 Sep 18 05:27 libstaden-read-dev_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 575808 Sep 18 05:27 libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 270608 Sep 18 05:27 libstaden-read14t64_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2754072 Sep 18 05:27 staden-io-lib-examples_1.15.0-1.1_all.deb -rw-r--r-- 1 jenkins jenkins 362604 Sep 18 05:27 staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 171216 Sep 18 05:27 staden-io-lib-utils_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 17208 Sep 18 05:27 staden-io-lib_1.15.0-1.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2534 Sep 18 05:27 staden-io-lib_1.15.0-1.1.dsc -rw-r--r-- 1 jenkins jenkins 8532 Sep 18 05:27 staden-io-lib_1.15.0-1.1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9414 Sep 18 05:27 staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 3122 Sep 18 05:27 staden-io-lib_1.15.0-1.1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1356 Sep 18 05:27 staden-io-lib_1.15.0-1.1_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b2: total 4888 -rw-rw-r-- 1 jenkins jenkins 449733 Sep 18 05:44 build.log -rw-r--r-- 1 jenkins jenkins 349800 Sep 18 05:44 libstaden-read-dev_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 575808 Sep 18 05:44 libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 270608 Sep 18 05:44 libstaden-read14t64_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2754072 Sep 18 05:44 staden-io-lib-examples_1.15.0-1.1_all.deb -rw-r--r-- 1 jenkins jenkins 362604 Sep 18 05:44 staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 171216 Sep 18 05:44 staden-io-lib-utils_1.15.0-1.1_amd64.deb -rw-r--r-- 1 jenkins jenkins 17208 Sep 18 05:44 staden-io-lib_1.15.0-1.1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2534 Sep 18 05:44 staden-io-lib_1.15.0-1.1.dsc -rw-rw-r-- 1 jenkins jenkins 8532 Sep 18 05:44 staden-io-lib_1.15.0-1.1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 9414 Sep 18 05:44 staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 3122 Sep 18 05:44 staden-io-lib_1.15.0-1.1_amd64.changes -rw-rw-r-- 1 jenkins jenkins 1356 Sep 18 05:44 staden-io-lib_1.15.0-1.1_source.changes Thu Sep 18 05:44:34 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Sep 18 05:44:34 UTC 2025 I: staden-io-lib_1.15.0-1.1_amd64.changes: Format: 1.8 Date: Fri, 01 Mar 2024 12:46:06 +0000 Source: staden-io-lib Binary: libstaden-read-dev libstaden-read14t64 libstaden-read14t64-dbgsym staden-io-lib-examples staden-io-lib-utils staden-io-lib-utils-dbgsym Architecture: amd64 all Version: 1.15.0-1.1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Benjamin Drung Description: libstaden-read-dev - development files for libstaden-read libstaden-read14t64 - Staden library for reading and writing DNA sequencing results staden-io-lib-examples - programs for manipulating DNA sequencing files (usage examples) staden-io-lib-utils - programs for manipulating DNA sequencing files Closes: 1063189 Changes: staden-io-lib (1.15.0-1.1) unstable; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. Closes: #1063189 Checksums-Sha1: 5c52f5b671ccda4226aab8e6e10a45c5e3c499ab 349800 libstaden-read-dev_1.15.0-1.1_amd64.deb 5771b5621aa0e9ef9105ccf7c8fe52227e5af0fc 575808 libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb 4be63a6582b2b4bb281c37cd08cd826f5d738993 270608 libstaden-read14t64_1.15.0-1.1_amd64.deb 8dc24f146d8fbe15c17ab863ce1027499a651a08 2754072 staden-io-lib-examples_1.15.0-1.1_all.deb c96a2ba70933986c4f05abf4be606c588d3e8a31 362604 staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb e1f9670a1116c8aa3031e0c0e4daaeaa4d3a4c84 171216 staden-io-lib-utils_1.15.0-1.1_amd64.deb 7136a52d1cc4e8e7d6a52e729f2e7646ae36d141 8532 staden-io-lib_1.15.0-1.1_amd64.buildinfo Checksums-Sha256: f261f0ec174e59efa8ea754eed6106f544418731a110a4bdc3baa61d7e6572a8 349800 libstaden-read-dev_1.15.0-1.1_amd64.deb 791f2255865930af95d837c86e2a93b8ff123e3984ab9053abc6d80c19557fd8 575808 libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb 8796275fb484c99b839ffcfba77603debc08f8c40418416fd5478e42577f301e 270608 libstaden-read14t64_1.15.0-1.1_amd64.deb 661d7d7e96ed1203227e8c8a49db35767d9351b8a96dd52d4698e6143191f270 2754072 staden-io-lib-examples_1.15.0-1.1_all.deb 71a988d098477c86988f0a57152a4435b1de5ba0d79ea446a47a7cb21cd2699e 362604 staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb 9a5e327eda45b63341f520142e4926f5b437129e7b0eaca1f41ab91cb8f0df76 171216 staden-io-lib-utils_1.15.0-1.1_amd64.deb ea631340fcce22cfa7056d8e35fb60aa3cdaa8be8ded7ad58c1edcda9a1de8da 8532 staden-io-lib_1.15.0-1.1_amd64.buildinfo Files: c17c90c80a5d8b29fae30f0ee98dc3b3 349800 libdevel optional libstaden-read-dev_1.15.0-1.1_amd64.deb 431f5ad8a3da7900a45c52caf0c34359 575808 debug optional libstaden-read14t64-dbgsym_1.15.0-1.1_amd64.deb 4364d1fb4706f894e8ecfa45b8c93f75 270608 libs optional libstaden-read14t64_1.15.0-1.1_amd64.deb c9d97d991aa738b9cb5a7311e5c8ad4d 2754072 science optional staden-io-lib-examples_1.15.0-1.1_all.deb 69cdc3a1082dc4cffce60c043972a020 362604 debug optional staden-io-lib-utils-dbgsym_1.15.0-1.1_amd64.deb 5e3a4570d0b530bc5a61cebde6797c7a 171216 science optional staden-io-lib-utils_1.15.0-1.1_amd64.deb a654d75e5e14e9edf0d7be7055633b68 8532 science optional staden-io-lib_1.15.0-1.1_amd64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/staden-io-lib_1.15.0-1.1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/staden-io-lib_1.15.0-1.1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/staden-io-lib_1.15.0-1.1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/staden-io-lib_1.15.0-1.1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/staden-io-lib_1.15.0-1.1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/staden-io-lib_1.15.0-1.1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 05:27:53.346757305 +0000 +++ b2/build.log 2025-09-18 05:44:34.256010494 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 17 17:15:12 -12 2025 -I: pbuilder-time-stamp: 1758172512 +I: Current time: Thu Oct 22 01:50:54 +14 2026 +I: pbuilder-time-stamp: 1792583454 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1480077/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 21 11:51 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d756168538d94e1880fc38905fadc9ff' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1480077' - PS1='# ' - PS2='> ' + INVOCATION_ID=75a94e6b188e4d0bb5aea7e798930642 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3176574 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/pbuilderrc_B1pV --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b1 --logfile b1/build.log staden-io-lib_1.15.0-1.1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/pbuilderrc_TMiw --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b2 --logfile b2/build.log staden-io-lib_1.15.0-1.1.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1480077/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -213,7 +245,7 @@ Get: 89 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] -Fetched 31.9 MB in 13s (2476 kB/s) +Fetched 31.9 MB in 8s (3801 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -592,7 +624,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/staden-io-lib-1.15.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../staden-io-lib_1.15.0-1.1_source.changes +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/staden-io-lib-1.15.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../staden-io-lib_1.15.0-1.1_source.changes dpkg-buildpackage: info: source package staden-io-lib dpkg-buildpackage: info: source version 1.15.0-1.1 dpkg-buildpackage: info: source distribution unstable @@ -838,160 +874,160 @@ make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' Making all in io_lib make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scf_extras.c -o libstaden_read_la-scf_extras.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -fPIC -DPIC -o .libs/libstaden_read_la-translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -fPIC -DPIC -o .libs/libstaden_read_la-fpoint.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fpoint.c -o libstaden_read_la-fpoint.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOABI.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -fPIC -DPIC -o .libs/libstaden_read_la-expFileIO.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c expFileIO.c -o libstaden_read_la-expFileIO.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOPlain.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-misc_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c misc_scf.c -o libstaden_read_la-misc_scf.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-read_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c read_scf.c -o libstaden_read_la-read_scf.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c write_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-write_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c write_scf.c -o libstaden_read_la-write_scf.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c libtool: compile: gcc 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c srf.c -fPIC -DPIC -o .libs/libstaden_read_la-srf.o libtool: compile: gcc -DHAVE_CONFIG_H 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-fcf-protection -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -fPIC -DPIC -o .libs/libstaden_read_la-error.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c error.c -o libstaden_read_la-error.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -fPIC -DPIC -o .libs/libstaden_read_la-files.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c files.c -o libstaden_read_la-files.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -fPIC -DPIC -o .libs/libstaden_read_la-find.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c find.c -o libstaden_read_la-find.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mach-io.c -fPIC -DPIC -o .libs/libstaden_read_la-mach-io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration 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-DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration 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libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c strings.c -fPIC -DPIC -o .libs/libstaden_read_la-strings.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -fPIC -DPIC -o .libs/libstaden_read_la-traceType.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -fPIC -DPIC -o .libs/libstaden_read_la-xalloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c xalloc.c -o libstaden_read_la-xalloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -fPIC -DPIC -o .libs/libstaden_read_la-vlen.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -fPIC -DPIC -o .libs/libstaden_read_la-hash_table.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -fPIC -DPIC -o .libs/libstaden_read_la-jenkins_lookup3.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration 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-D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 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-fcf-protection -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration 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../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 15:3:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/x86_64-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 15:3:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/x86_64-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -llzma -lbz2 libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -lcurl -lhtscodecs -lm -llzma -lbz2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.3 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.3" "libstaden-read.so") @@ -1002,118 +1038,118 @@ Making all in progs make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o convert_trace.o convert_trace.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o makeSCF.o makeSCF.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o extract_seq.o extract_seq.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o extract_qual.o 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scramble.o scramble.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_merge.o scram_merge.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_pileup.o scram_pileup.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_flagstat.o scram_flagstat.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o scram_test.o scram_test.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_size.o cram_size.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_filter.o cram_filter.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' Making all in tests make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cram_io_test.o cram_io_test.c -/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 +/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/staden-io-lib-1.15.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2 make[3]: Leaving directory '/build/reproducible-path/staden-io-lib-1.15.0/tests' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0' @@ -5037,7 +5073,7 @@ make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/io_lib' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.3 /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.3 libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.3 libstaden-read.so.14; }; }) libtool: install: (cd /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libstaden-read.so.14.1.3 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.3 libstaden-read.so; }; }) @@ -5053,7 +5089,7 @@ make[2]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' make[3]: Entering directory '/build/reproducible-path/staden-io-lib-1.15.0/progs' /usr/bin/mkdir -p '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' - /bin/bash ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/convert_trace /build/reproducible-path/staden-io-lib-1.15.0/debian/tmp/usr/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu' @@ -5236,12 +5272,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3176574/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1480077 and its subdirectories -I: Current time: Wed Sep 17 17:27:52 -12 2025 -I: pbuilder-time-stamp: 1758173272 +I: removing directory /srv/workspace/pbuilder/3176574 and its subdirectories +I: Current time: Thu Oct 22 02:07:33 +14 2026 +I: pbuilder-time-stamp: 1792584453 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/staden-io-lib_1.15.0-1.1.diff: 94.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/staden-io-lib_1.15.0-1.1.diff.gz b2/build.log: 92.9% -- replaced with stdout Compressing the 1st log... b1/build.log: 93.0% -- replaced with stdout Thu Sep 18 05:44:35 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_staden-io-lib_unstable_amd64_1758174275 + touch /var/log/reproducible-builds/diffoscope_stamp_staden-io-lib_unstable_amd64_1758174275 + RESULT=0 + systemd-run '--description=diffoscope on staden-io-lib/1.15.0-1.1 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_23-72371 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC --run-session -c jenkins-reproducible-unstable-diffoscope-4661d15f-5420-4bb4-93b7-89194519a7b4 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/dbd-tmp-qDguKSJ ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/staden-io-lib_1.15.0-1.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/staden-io-lib_1.15.0-1.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/staden-io-lib_1.15.0-1.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b1/staden-io-lib_1.15.0-1.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b2/staden-io-lib_1.15.0-1.1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_23-72371.service; invocation ID: a5d37d148d8f4ed8af9265ac52c3e58e # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/staden-io-lib_1.15.0-1.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/staden-io-lib_1.15.0-1.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/staden-io-lib_1.15.0-1.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b1/staden-io-lib_1.15.0-1.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.C8EnWTYC/b2/staden-io-lib_1.15.0-1.1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 210ms CPU time consumed: 168ms Memory peak: 18.1M (swap: 0B) _ _ _ _ _ _ ___| |_ __ _ __| | ___ _ __ (_) ___ | (_) |__ / __| __/ _` |/ _` |/ _ \ '_ \ _____| |/ _ \ _____| | | '_ \ \__ \ || (_| | (_| | __/ | | |_____| | (_) |_____| | | |_) | |___/\__\__,_|\__,_|\___|_| |_| |_|\___/ |_|_|_.__/ Thu Sep 18 05:44:35 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 05:44:35 UTC 2025 I: staden-io-lib from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 05:44:36] INFO: Starting at 2025-09-18 05:44:36.136858 [2025-09-18 05:44:36] INFO: Generating the pages of 1 package(s) [2025-09-18 05:44:36] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/staden-io-lib didn't produce a buildlog, even though it has been built. [2025-09-18 05:44:36] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/staden-io-lib didn't produce a buildlog, even though it has been built. [2025-09-18 05:44:36] INFO: Finished at 2025-09-18 05:44:36.417518, took: 0:00:00.280662 Thu Sep 18 05:44:36 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/staden-io-lib.html Thu Sep 18 05:44:36 UTC 2025 I: Removing signed staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc files: removed './b1/staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc' removed './b2/staden-io-lib_1.15.0-1.1_amd64.buildinfo.asc' 1758174276 amd64 unstable staden-io-lib Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/staden-io-lib_1.15.0-1.1.rbuild.log: 92.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/staden-io-lib_1.15.0-1.1.rbuild.log.gz [2025-09-18 05:44:36] INFO: Starting at 2025-09-18 05:44:36.769424 [2025-09-18 05:44:36] INFO: Generating the pages of 1 package(s) [2025-09-18 05:44:37] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/staden-io-lib didn't produce a buildlog, even though it has been built. [2025-09-18 05:44:37] INFO: Finished at 2025-09-18 05:44:37.041866, took: 0:00:00.272445 All cleanup done. Thu Sep 18 05:44:37 UTC 2025 - total duration: 0h 29m 32s. Thu Sep 18 05:44:37 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-jEEVsi9x, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 29min 33.868s CPU time consumed: 3.791s Memory peak: 52.1M (swap: 0B)