Mon Sep 8 00:12:52 UTC 2025 I: starting to build htslib/forky/amd64 on jenkins on '2025-09-08 00:12' Mon Sep 8 00:12:52 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_31/56735/console.log Mon Sep 8 00:12:52 UTC 2025 I: Downloading source for forky/htslib=1.22.1+ds2-1 --2025-09-08 00:12:53-- http://deb.debian.org/debian/pool/main/h/htslib/htslib_1.22.1%2bds2-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2473 (2.4K) [text/prs.lines.tag] Saving to: ‘htslib_1.22.1+ds2-1.dsc’ 0K .. 100% 252M=0s 2025-09-08 00:12:53 (252 MB/s) - ‘htslib_1.22.1+ds2-1.dsc’ saved [2473/2473] Mon Sep 8 00:12:53 UTC 2025 I: htslib_1.22.1+ds2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: htslib Binary: libhts3t64, libhts-dev, htslib-test, tabix Architecture: any all Version: 1.22.1+ds2-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://github.com/samtools/htslib Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, build-essential Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev Package-List: htslib-test deb science optional arch=all libhts-dev deb libdevel optional arch=any libhts3t64 deb libs optional arch=any tabix deb science optional arch=any Checksums-Sha1: ce3c0511527a8bc8a3327cf6aaa38b28ec271e0c 1593472 htslib_1.22.1+ds2.orig.tar.bz2 47a81c0b05b2700d0660b453fa5ddb3ded7e5cb4 22004 htslib_1.22.1+ds2-1.debian.tar.xz Checksums-Sha256: 911a26eb37943726c5f616bd8044144dbdcc0c127e8770f6b82ed0627f3dbd80 1593472 htslib_1.22.1+ds2.orig.tar.bz2 e97c8951ce5ff4d80c7dc3f2c0b8a4b73ddf18f7d219f2b15aaf104af4b28018 22004 htslib_1.22.1+ds2-1.debian.tar.xz Files: 435ce1c1b723732c43d0925889e2d3d4 1593472 htslib_1.22.1+ds2.orig.tar.bz2 ded83a10f428ad5a72615e496d651719 22004 htslib_1.22.1+ds2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmi5imkSHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+biGAYP/1aC/QvynNdNcVe3ikuDnnZFhSiQbj4k 3m39CS5oS5ZjJuNW2GaZvEZHcPWoUjb7bwjbkh9oee9D2fK8JezxAe5ILnB0PA6K BMfn9mzDcrLiJSSUk++wUzog79XIT2YW63l1wSc0MAtaJyNUJZomDjcvOCoQX/j0 7Rz77h6TkkO60isA7e30AKToL+u0SeNzD8MkiJDJbE0NxhxGgd/zhM8w+RlK3VnM MbpjepUwV2GxD0IIEt6hPgF6cbZWR4guBQPClrvb7ZYpn5uIf19vE9xMyDw6mRB8 Bz892I2NyYsotOtsa+i7qy/SNKMtXdYB2pCglpJPOcqsx6DFUqsC4QeO2K14YiDA roBlRukKPfrOFyc+uXvXInyW4BiROux7fV7EBhz8msfrN9MQX7K8rJzLt7hB+gCt +CqZEepEOldbdMCRGpD/YBD01BvtdP87MJeqkeoqVbpz5+yuG3TYtalYQmTut6ky FmFXCUjsb5TySqRMB09sOUyqd+raWjjLyU/J/PeA5Jy1VrctWvGkeTiYCQjhroG2 f+lZxtxqBholSfwMXGTwc4ayDDUM3Rj3eudCEjeB2l6qVsOESLTZfGwtZKNEbg5g vEXGVqxpUozr3FvisF3Lk7HS81k1r9juqr6Ss5S3cjh8WFrX1wskJIcu0y8MicwV tCS6yVoks8/2 =DUBu -----END PGP SIGNATURE----- Mon Sep 8 00:12:53 UTC 2025 I: Checking whether the package is not for us Mon Sep 8 00:12:53 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Sep 8 00:12:53 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Sep 8 00:17:35 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 7 12:12:54 -12 2025 I: pbuilder-time-stamp: 1757290374 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [htslib_1.22.1+ds2-1.dsc] I: copying [./htslib_1.22.1+ds2.orig.tar.bz2] I: copying [./htslib_1.22.1+ds2-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./htslib_1.22.1+ds2-1.dsc: no acceptable signature found dpkg-source: info: extracting htslib in htslib-1.22.1+ds2 dpkg-source: info: unpacking htslib_1.22.1+ds2.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.22.1+ds2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11543/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='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1b941b4d19a54b8587e3a0eb4d670258' 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='11543' 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.11Dssgvs/pbuilderrc_fp7M --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.11Dssgvs/b1 --logfile b1/build.log htslib_1.22.1+ds2-1.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/11543/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), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-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 ... 19897 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 libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on libhtscodecs-dev; however: Package libhtscodecs-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} 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} libdeflate-dev{a} libdeflate0{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, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 31.8 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-2 [95.0 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.14.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.14.2-1 [8768 B] Get: 24 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 35 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libssl-dev amd64 3.5.2-1 [2957 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libcurl4-gnutls-dev amd64 8.15.0-1 [504 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Fetched 31.8 MB in 2s (18.6 MB/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 ... 19897 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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Preparing to unpack .../89-libhtscodecs2_1.6.1-2_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.1-2) ... Selecting previously unselected package libhtscodecs-dev:amd64. Preparing to unpack .../90-libhtscodecs-dev_1.6.1-2_amd64.deb ... Unpacking libhtscodecs-dev:amd64 (1.6.1-2) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../91-liblzma-dev_5.8.1-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.8.1-1) ... Setting up libhtscodecs2:amd64 (1.6.1-2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-1.1) ... Setting up bsdextrautils (2.41.1-2) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... 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 (3.5.2-1) ... Setting up autopoint (0.23.1-2) ... 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 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... 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 (1.11.0-1) ... 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 libdeflate-dev:amd64 (1.23-2) ... 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 (1.14.2-1) ... 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 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... 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 (1.14.2-1) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-3) ... 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 (3.8.9-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... 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 (8.15.0-1) ... 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/htslib-1.22.1+ds2/ && 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 > ../htslib_1.22.1+ds2-1_source.changes dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.22.1+ds2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean dh_auto_clean make -j40 distclean make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* \ test/longrefs/*.tmp.* test/ref_cache/*.tmp.* test/tabix/*.tmp.* \ test/bgzf_boundaries/*.tmp.* test/*/FAIL* \ header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -rf htscodecs/tests/test.out rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico rm -f hts-object-files rm -f htscodecs/tests/*.o rm -f ref_cache/*.o rm -f libhts.a annot-tsv bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/pileup_mod test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_faidx test/test_kfunc test/test_khash test/test_kstring test/test_mod test/test_nibbles test/test_realn test/test-regidx test/test_str2int test/test_time_funcs test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/test-bcf_set_variant_type test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk rm -rf autom4te.cache make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' rm -rf test_backup/ make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3t64/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/x86_64-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib' ./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 --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/x86_64-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib 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 for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed 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 whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... yes checking whether __cpuid_count is declared... yes checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt checking C compiler flags needed for avx2... -mavx2 -mpopcnt checking C compiler flags needed for avx512f... -mavx512f -mpopcnt checking for working __builtin_cpu_supports("ssse3")... yes checking for working __attribute__((target("ssse3")))... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for getpagesize... yes checking for working mmap... (cached) yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking for getauxval... yes checking for elf_aux_info... no checking for posix_memalign... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for htscodecs/rANS_static4x16.h... yes checking for rans_compress_bound_4x16 in -lhtscodecs... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for CMSG_LEN... yes checking for epoll... yes (edge triggered) checking for sendfile... yes, Linux-style checking whether EHOSTDOWN is declared... yes checking whether ENONET is declared... yes checking whether AI_V4MAPPED is declared... yes checking whether AI_ADDRCONFIG is declared... yes checking whether the compiler accepts -Wextra... yes checking whether the compiler accepts -Wformat... yes checking whether the compiler accepts -Wformat=2... yes checking whether the compiler accepts -Wconversion... yes checking whether the compiler accepts -Wtrampolines... yes checking whether the compiler accepts -Wstrict-aliasing... yes checking whether the compiler accepts -fstack-clash-protection... yes checking whether the compiler accepts -fstack-protector-strong... yes checking whether the compiler accepts -fcf-protection=full... yes checking whether the compiler accepts -mbranch-protection=standard... no checking whether the compiler accepts -fno-delete-null-pointer-checks... yes checking whether the compiler accepts -Wl,-z,noexecstack... yes checking whether the compiler accepts -Wl,-z,relro... yes checking whether the compiler accepts -Wl,-z,now... yes checking whether the compiler accepts -Wl,--as-needed... yes checking whether the compiler accepts -Wl,--no-copy-dt-needed-entries... yes checking whether the compiler accepts -Wl,-z,nodlopen... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_external.mk to htscodecs.mk make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu make -j40 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.22.1"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2' \ '-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects' \ '-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ > config_vars.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o simd.o simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o simd.pico simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o annot-tsv.o annot-tsv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_faidx.o test/test_faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_khash.o test/test_khash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_mod.o test/test_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_nibbles.o test/test_nibbles.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > htslib-uninstalled.pc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/cmsg_wrap.o ref_cache/cmsg_wrap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/http_parser.o ref_cache/http_parser.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/listener.o ref_cache/listener.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/log_files.o ref_cache/log_files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/main.o ref_cache/main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/misc.o ref_cache/misc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/ping.o ref_cache/ping.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_epoll.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/poll_wrap_poll.o ref_cache/poll_wrap_poll.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/ref_files.o ref_cache/ref_files.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/request_handler.o ref_cache/request_handler.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/sendfile_wrap.o ref_cache/sendfile_wrap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/server.o ref_cache/server.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/transaction.o ref_cache/transaction.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -Wextra -Wformat -Wformat=2 -Wconversion -Wtrampolines -Wstrict-aliasing -fstack-clash-protection -fstack-protector-strong -fcf-protection=full -fno-delete-null-pointer-checks -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ref_cache/upstream.o ref_cache/upstream.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -Wl,-z,noexecstack -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,nodlopen -o ref_cache/ref-cache ref_cache/cmsg_wrap.o ref_cache/http_parser.o ref_cache/listener.o ref_cache/log_files.o ref_cache/main.o ref_cache/misc.o ref_cache/ping.o ref_cache/poll_wrap_epoll.o ref_cache/poll_wrap_poll.o ref_cache/ref_files.o ref_cache/request_handler.o ref_cache/sendfile_wrap.o ref_cache/server.o ref_cache/transaction.o ref_cache/upstream.o cram/pooled_alloc.o md5.o -lcurl gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico simd.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread make[2]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu \ || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j40 test "TESTSUITEFLAGS=-j40 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 41 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && \ if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ else \ REF_PATH=: ./test.pl --ref-cache-bin ../ref_cache/ref-cache ${TEST_OPTS:-} ; \ fi bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 14 -x /tmp/DF7_OrYhHY/index.bam.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 0 -x /tmp/DF7_OrYhHY/index.bam.bai /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -b /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/DF7_OrYhHY/index.sam.gz.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/DF7_OrYhHY/index.sam.gz.bai /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -b /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/DF7_OrYhHY/index.sam.gz.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/DF7_OrYhHY/index.sam.gz.bai /build/reproducible-path/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -b /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -C -x /tmp/DF7_OrYhHY/index.cram.crai /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.cram .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index /tmp/DF7_OrYhHY/index.cram .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -b -m 14 -x /tmp/DF7_OrYhHY/index.bcf.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.vcf > /tmp/DF7_OrYhHY/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 14 -x /tmp/DF7_OrYhHY/index.vcf.gz.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.vcf > /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -l 0 -z -m 0 -x /tmp/DF7_OrYhHY/index.vcf.gz.tbi /build/reproducible-path/htslib-1.22.1+ds2/test/index.vcf > /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -t /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/tabix /tmp/DF7_OrYhHY/index.vcf.gz##idx##/tmp/DF7_OrYhHY/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 1:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 1:2000000-2000000 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 2:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 2:2000000-2000000 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 14 -x /tmp/DF7_OrYhHY/index.bam.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 0 -x /tmp/DF7_OrYhHY/index.bam.bai /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -b /tmp/DF7_OrYhHY/index.bam .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/DF7_OrYhHY/index.sam.gz.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/DF7_OrYhHY/index.sam.gz.bai /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -b /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/DF7_OrYhHY/index.sam.gz.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/DF7_OrYhHY/index.sam.gz.bai /build/reproducible-path/htslib-1.22.1+ds2/test/index_dos.sam > /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -b /tmp/DF7_OrYhHY/index.sam.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -C -x /tmp/DF7_OrYhHY/index.cram.crai /build/reproducible-path/htslib-1.22.1+ds2/test/index.sam > /tmp/DF7_OrYhHY/index.cram .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index /tmp/DF7_OrYhHY/index.cram .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -b -m 14 -x /tmp/DF7_OrYhHY/index.bcf.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.vcf > /tmp/DF7_OrYhHY/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.bcf .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 14 -x /tmp/DF7_OrYhHY/index.vcf.gz.csi /build/reproducible-path/htslib-1.22.1+ds2/test/index.vcf > /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -@4 -l 0 -z -m 0 -x /tmp/DF7_OrYhHY/index.vcf.gz.tbi /build/reproducible-path/htslib-1.22.1+ds2/test/index.vcf > /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -t /tmp/DF7_OrYhHY/index.vcf.gz .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/tabix /tmp/DF7_OrYhHY/index.vcf.gz##idx##/tmp/DF7_OrYhHY/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 1:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 1:2000000-2000000 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 2:1000000-1000000 .. ok test_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /tmp/DF7_OrYhHY/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#bounds_er.tmp.cram.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.bam ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds_er.tmp.cram.sam > c1#bounds_er.tmp.cram.tmp.cram ./test_view -@4 -D c1#bounds_er.tmp.cram.tmp.cram > c1#bounds_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds_er.tmp.cram.tmp.bam > c1#bounds_er.tmp.cram.tmp.bam.cram ./test_view -@4 c1#bounds_er.tmp.cram.tmp.bam.cram > c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#u.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#u.sam > xx#u.tmp.bam ./test_view -@4 xx#u.tmp.bam > xx#u.tmp.bam.sam_ ./compare_sam.pl xx#u.sam xx#u.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#u.sam > xx#u.tmp.cram ./test_view -@4 -D xx#u.tmp.cram > xx#u.tmp.cram.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#u.tmp.bam > xx#u.tmp.bam.cram ./test_view -@4 xx#u.tmp.bam.cram > xx#u.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#u.sam xx#u.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference "CHROMOSOME_I" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam ./test_view -@4 -C -p c1#bounds_er.tmp.cram c1#bounds.sam [W::cram_get_ref] Failed to populate reference "c1" [W::cram_get_ref] See https://www.htslib.org/doc/reference_seqs.html for further suggestions [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p c1#bounds_er.tmp.cram.sam c1#bounds_er.tmp.cram ./compare_sam.pl c1#bounds.sam c1#bounds_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/reproducible-path/htslib-1.22.1+ds2/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /build/reproducible-path/htslib-1.22.1+ds2/test/test-vcf-api /tmp/DF7_OrYhHY/test-vcf-api.bcf .. ok test_bcf2vcf: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /build/reproducible-path/htslib-1.22.1+ds2/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/reproducible-path/htslib-1.22.1+ds2/test/test-vcf-sweep /tmp/DF7_OrYhHY/test-vcf-api.bcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.22.1+ds2/htsfile -ch /build/reproducible-path/htslib-1.22.1+ds2/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.22.1+ds2/htsfile -c /build/reproducible-path/htslib-1.22.1+ds2/test/formatcols.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.22.1+ds2/htsfile -c /build/reproducible-path/htslib-1.22.1+ds2/test/noroundtrip.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.22.1+ds2/htsfile -c /build/reproducible-path/htslib-1.22.1+ds2/test/formatmissing.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.22.1+ds2/htsfile -c /build/reproducible-path/htslib-1.22.1+ds2/test/vcf_meta_meta.vcf .. ok test_vcf_various: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view /build/reproducible-path/htslib-1.22.1+ds2/test/modhdr.vcf.gz chr22:1-2 .. ok test_vcf_44: /build/reproducible-path/htslib-1.22.1+ds2/htsfile -c /build/reproducible-path/htslib-1.22.1+ds2/test/vcf44_1.vcf .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 74452500 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 34270147 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 11108528 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 42233895 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 8111117 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 85644070 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 49879942 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 47881429 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 69081244 .. ok test-bcf-sr: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr.pl -t /tmp/DF7_OrYhHY -s 83459376 .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.b.vcf /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/DF7_OrYhHY/no_index_1.err .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/DF7_OrYhHY/no_index_2.out 2> /tmp/DF7_OrYhHY/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/DF7_OrYhHY/no_index_3.out 2> /tmp/DF7_OrYhHY/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr --no-index -p all --args /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.rec_order.vcf /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/merge.noidx.a.vcf > /tmp/DF7_OrYhHY/no_index_4.out 2> /tmp/DF7_OrYhHY/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -b -p /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf -x /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf.csi /build/reproducible-path/htslib-1.22.1+ds2/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_1.out.vcf -r '1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_2.out.vcf -r '1:1-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_4.out.vcf -r '1:1-1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_5.out.vcf -r '{1:1}' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_14.out.vcf -t '1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_15.out.vcf -t '1:1-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_17.out.vcf -t '1:1-1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_18.out.vcf -t '{1:1}' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-sr -O vcf -o /tmp/DF7_OrYhHY/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/DF7_OrYhHY/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok .. ok test_command: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf-translate - .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/DF7_OrYhHY/headernul0.bam .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/DF7_OrYhHY/headernul1.bam .. ok test_convert_padded_header: /build/reproducible-path/htslib-1.22.1+ds2/test/test_view -t ce.fa -C /tmp/DF7_OrYhHY/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/reproducible-path/htslib-1.22.1+ds2/bgzip -I /build/reproducible-path/htslib-1.22.1+ds2/test/bgziptest.txt.tmp.gz.gzi -c -g /build/reproducible-path/htslib-1.22.1+ds2/test/bgziptest.txt .. ok test-logging: /build/reproducible-path/htslib-1.22.1+ds2/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/reproducible-path/htslib-1.22.1+ds2 /build/reproducible-path/htslib-1.22.1+ds2/test/with-shlib.sh /build/reproducible-path/htslib-1.22.1+ds2/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn01.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -a -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn01.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -a -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -e -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn01.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn01.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -e -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -r -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn02-r.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -a -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn02_exp.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn02.fa -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn02_exp-a.sam -o - .. ok test_realn: /build/reproducible-path/htslib-1.22.1+ds2/test/test_realn -f /build/reproducible-path/htslib-1.22.1+ds2/test/realn03.fa -e -i /build/reproducible-path/htslib-1.22.1+ds2/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /build/reproducible-path/htslib-1.22.1+ds2/test/test-bcf_set_variant_type .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -c chr,beg,end -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl,value:overlap,value -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -O 0.5 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -rO 0.5 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.1.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.2.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.3.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl:overlap -a nbp,frac -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.4.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.5.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.6.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.7.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.8.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.9.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -f smpl -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -x -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -x -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -x -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -f smpl -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -x -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -x -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.10.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -m smpl -x -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.12.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 11:11 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -s /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt .. ok run_annot_tsv: cat /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/src.14.txt | /build/reproducible-path/htslib-1.22.1+ds2/annot-tsv -c 1,2,3 -C 01:01 -t /build/reproducible-path/htslib-1.22.1+ds2/test/annot-tsv/dst.14.txt .. ok ref-cache: ./test_view -C -p ref_cache/ce_m5.sam.tmp.cram ref_cache/ce_m5.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.2.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.2.sam ./test_view -p ref_cache/ce_m5.sam.tmp.cram.3.sam ref_cache/ce_m5.sam.tmp.cram ./compare_sam.pl --nomd ref_cache/ce_m5.sam ref_cache/ce_m5.sam.tmp.cram.3.sam .. ok Number of tests: total .. 352 passed .. 352 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' rm -fr -- /tmp/dh-xdg-rundir-e8J5Ks98 make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3t64/ debian/libhts3t64/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/htslib-test/ debian/htslib-test/ debian/.debhelper/generated/tabix/ debian/tabix/ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/reproducible-path/htslib-1.22.1+ds2/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.22.1" \ libdir=/usr/lib/x86_64-linux-gnu install -m0755 -d /build/reproducible-path/htslib-1.22.1\+ds2/debian/tmp make -j40 install DESTDIR=/build/reproducible-path/htslib-1.22.1\+ds2/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/htslib-1.22.1+ds2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.22.1 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' mkdir -p -m 755 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/bin /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/include /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/include/htslib /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man5 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man7 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig if test -n "/usr/lib/x86_64-linux-gnu/htslib"; then mkdir -p -m 755 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 libhts.so /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.22.1#g' htslib.pc.tmp > /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc chmod 644 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.22.1 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.22.1 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 install -p annot-tsv bgzip htsfile tabix ref_cache/ref-cache /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 if test "xref_cache/ref-cache" != "x" ; then \ install -p -m 644 ref_cache/ref-cache.1 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man1 ; \ fi install -p -m 644 faidx.5 sam.5 vcf.5 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/reproducible-path/htslib-1.22.1+ds2/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals rm -f -r test mv test_backup test make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_install install -m0755 -d debian/libhts3t64/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/htslib debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 debian/libhts3t64/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts3t64/usr/share/man/man5 cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man5/ install -m0755 -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -m0755 -d debian/htslib-test/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/tests/run-unit-test debian/htslib-test/usr/share/doc/libhts-dev/ install -m0755 -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./annot-tsv.c ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./builddir_vars.mk.in ./config.h.in ./config.mk.in ./configure.ac ./errmod.c ./faidx.c ./fuzz_settings.h ./header.c ./header.h ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_s3.c ./hfile_s3_write.c ./hts.c ./hts_expr.c ./hts_internal.h ./hts_os.c ./hts_time_funcs.h ./htscodecs.mk ./htscodecs_bundled.mk ./htscodecs_external.mk ./htsfile.c ./htslib.mk ./htslib.pc.in ./htslib_static.mk ./htslib_vars.mk ./kfunc.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./region.c ./sam.c ./sam_internal.h ./sam_mods.c ./simd.c ./synced_bcf_reader.c ./tabix.c ./tbx.c ./textutils.c ./textutils_internal.h ./thread_pool.c ./thread_pool_internal.h ./vcf.c ./vcf_sweep.c ./vcfutils.c ./version.sh debian/htslib-test/usr/share/htslib-test/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.c ./cram/cram_codecs.h ./cram/cram_decode.c ./cram/cram_decode.h ./cram/cram_encode.c ./cram/cram_encode.h ./cram/cram_external.c ./cram/cram_index.c ./cram/cram_index.h ./cram/cram_io.c ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.c ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.c ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.c ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.c ./cram/pooled_alloc.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/m4 cp --reflink=auto -a ./m4/hts_check_compile_flags_needed.m4 ./m4/hts_hide_dynamic_syms.m4 ./m4/hts_prog_cc_warnings.m4 ./m4/pkg.m4 debian/htslib-test/usr/share/htslib-test/m4/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/ref_cache cp --reflink=auto -a ./ref_cache/cmsg_wrap.c ./ref_cache/cmsg_wrap.h ./ref_cache/http_parser.c ./ref_cache/http_parser.h ./ref_cache/listener.c ./ref_cache/listener.h ./ref_cache/log_files.c ./ref_cache/log_files.h ./ref_cache/main.c ./ref_cache/misc.c ./ref_cache/misc.h ./ref_cache/options.h ./ref_cache/ping.c ./ref_cache/ping.h ./ref_cache/poll_wrap.h ./ref_cache/poll_wrap_epoll.c ./ref_cache/poll_wrap_poll.c ./ref_cache/ref_files.c ./ref_cache/ref_files.h ./ref_cache/request_handler.c ./ref_cache/request_handler.h ./ref_cache/sendfile_wrap.c ./ref_cache/sendfile_wrap.h ./ref_cache/server.c ./ref_cache/server.h ./ref_cache/transaction.c ./ref_cache/transaction.h ./ref_cache/types.h ./ref_cache/upstream.c ./ref_cache/upstream.h debian/htslib-test/usr/share/htslib-test/ref_cache/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/annot-tsv ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/base_mods ./test/bcf-sr ./test/bgzf_boundaries ./test/bgziptest.txt ./test/bgziptest.txt.gz ./test/bgziptest.txt.gz.gzi ./test/c1\#bounds.sam ./test/c1\#clip.sam ./test/c1\#noseq.sam ./test/c1\#pad1.sam ./test/c1\#pad2.sam ./test/c1\#pad3.sam ./test/c1\#unknown.sam ./test/c1.fa ./test/c1.fa.fai ./test/c2\#pad.sam ./test/c2.fa ./test/c2.fa.fai ./test/ce\#1.sam ./test/ce\#1000.sam ./test/ce\#2.sam ./test/ce\#5.sam ./test/ce\#5b.sam ./test/ce\#5b_java.cram ./test/ce\#large_seq.sam ./test/ce\#supp.sam ./test/ce\#tag_depadded.sam ./test/ce\#tag_padded.sam ./test/ce\#unmap.sam ./test/ce\#unmap1.sam ./test/ce\#unmap2.sam ./test/ce.fa ./test/ce.fa.fai ./test/colons.bam ./test/colons.bam.bai ./test/compare_sam.pl ./test/cross_validate.sh ./test/emptyfile ./test/faidx ./test/fastq ./test/fastqs_README.txt ./test/fieldarith.c ./test/fieldarith.sam ./test/formatcols.vcf ./test/formatmissing-out.vcf ./test/formatmissing.vcf ./test/fuzz ./test/header_syms.pl ./test/hfile.c ./test/hts_endian.c ./test/index.bam.bai ./test/index.bam.csi ./test/index.bcf.csi ./test/index.cram.crai ./test/index.sam ./test/index.sam.gz.bai ./test/index.sam.gz.csi ./test/index.vcf ./test/index.vcf.gz.csi ./test/index.vcf.gz.tbi ./test/index2.sam ./test/index_dos.sam ./test/longrefs ./test/maintainer ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./test/modhdr.expected.vcf ./test/modhdr.vcf.gz ./test/modhdr.vcf.gz.csi ./test/mpileup ./test/no_hdr_sq_1.bam ./test/no_hdr_sq_1.bam.csi ./test/no_hdr_sq_1.expected.sam ./test/noroundtrip-out.vcf ./test/noroundtrip.vcf ./test/pileup.c ./test/pileup_mod.c ./test/plugins-dlhts.c ./test/range.bam ./test/range.bam.bai ./test/range.cram ./test/range.cram.crai ./test/range.out ./test/range.out2 ./test/realn01.fa ./test/realn01.fa.fai ./test/realn01.sam ./test/realn01_exp-a.sam ./test/realn01_exp-e.sam ./test/realn01_exp.sam ./test/realn02-r.sam ./test/realn02.fa ./test/realn02.fa.fai ./test/realn02.sam ./test/realn02_exp-a.sam ./test/realn02_exp-e.sam ./test/realn02_exp.sam ./test/realn03.fa ./test/realn03.fa.fai ./test/realn03.sam ./test/realn03_exp.sam ./test/ref_cache ./test/sam.c ./test/sam_filter ./test/simple_test_driver.sh ./test/tabix ./test/tabix.out ./test/test-bcf-sr.c ./test/test-bcf-sr.pl ./test/test-bcf-translate.c ./test/test-bcf-translate.out ./test/test-bcf_set_variant_type.c ./test/test-logging.pl ./test/test-parse-reg.c ./test/test-regidx.c ./test/test-vcf-api.c ./test/test-vcf-api.out ./test/test-vcf-hdr-in.vcf ./test/test-vcf-hdr.out ./test/test-vcf-sweep.c ./test/test-vcf-sweep.out ./test/test.pl ./test/test_bgzf.c ./test/test_expr.c ./test/test_faidx.c ./test/test_index.c ./test/test_introspection.c ./test/test_kfunc.c ./test/test_khash.c ./test/test_kstring.c ./test/test_mod.c ./test/test_nibbles.c ./test/test_realn.c ./test/test_str2int.c ./test/test_time_funcs.c ./test/test_view.c ./test/thrash_threads1.c ./test/thrash_threads2.c ./test/thrash_threads3.c ./test/thrash_threads4.c ./test/thrash_threads5.c ./test/thrash_threads6.c ./test/thrash_threads7.c ./test/thread_pool.md ./test/usepublic.cpp ./test/vcf44_1.expected ./test/vcf44_1.vcf ./test/vcf_meta_meta.vcf ./test/with-shlib.sh ./test/xx\#MD.sam ./test/xx\#MD2.sam ./test/xx\#blank.sam ./test/xx\#large_aux.sam ./test/xx\#large_aux2.sam ./test/xx\#large_aux_java.cram ./test/xx\#minimal.sam ./test/xx\#pair.sam ./test/xx\#repeated.sam ./test/xx\#rg.sam ./test/xx\#tlen.sam ./test/xx\#tlen2.sam ./test/xx\#triplet.sam ./test/xx\#u.sam ./test/xx\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ install -m0755 -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules execute_after_dh_install-indep make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_installdocs install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/copyright debian/libhts3t64/usr/share/doc/libhts3t64/copyright install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so: No such file or directory make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_installchangelogs NEWS install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/.debhelper/generated/libhts3t64/dh_installchangelogs.dch.trimmed debian/libhts3t64/usr/share/doc/libhts3t64/changelog.Debian install -p -m0644 NEWS debian/libhts3t64/usr/share/doc/libhts3t64/changelog make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_installman install -m0755 -d debian/libhts3t64/usr/share/man/man7/ install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/sam.5 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/htsfile.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 mv debian/libhts3t64/usr/share/man/man5/vcf.5.dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/vcf.5 mv debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 chmod 0644 -- debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1 chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 chmod 0644 -- debian/tabix/usr/share/man/man1/htsfile.1 mv debian/libhts3t64/usr/share/man/man5/faidx.5.dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/faidx.5 mv debian/libhts3t64/usr/share/man/man5/sam.5.dh-new debian/libhts3t64/usr/share/man/man5/sam.5 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/sam.5 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1 dh_lintian install -m0755 -d debian/libhts-dev/usr/share/lintian/overrides install -p -m0644 debian/libhts-dev.lintian-overrides debian/libhts-dev/usr/share/lintian/overrides/libhts-dev install -m0755 -d debian/htslib-test/usr/share/lintian/overrides install -p -m0644 debian/htslib-test.lintian-overrides debian/htslib-test/usr/share/lintian/overrides/htslib-test dh_perl mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link rm -f debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.3 ln -s libhts.so.1.22.1 debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so ln -s libhts.so.1.22.1 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so rm -f debian/htslib-test/usr/share/htslib-test/htscodecs.mk ln -s htscodecs_external.mk debian/htslib-test/usr/share/htslib-test/htscodecs.mk install -m0755 -d debian/tabix/usr/share/man/man1 rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism Using 1756986990 as canonical time Normalizing debian/htslib-test/usr/share/htslib-test/test/bgziptest.txt.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/htslib-test/usr/share/htslib-test/test/modhdr.vcf.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/libhts3t64 cd debian/libhts-dev cd debian/htslib-test cd debian/tabix chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 chmod a-x usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian gzip -9nf usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 cd '/build/reproducible-path/htslib-1.22.1+ds2' cd '/build/reproducible-path/htslib-1.22.1+ds2' cd '/build/reproducible-path/htslib-1.22.1+ds2' cd '/build/reproducible-path/htslib-1.22.1+ds2' dh_fixperms find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/htslib-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/include debian/libhts-dev/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libhts3t64 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libhts3t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' debian/rules execute_before_dh_missing make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_missing dh_dwz -a install -m0755 -d debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -- debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 install -m0755 -d debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix dwz: debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1: DWARF compression not beneficial - old size 985268 new size 1008720 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug debian/rules override_dh_strip make[1]: Entering directory '/build/reproducible-path/htslib-1.22.1+ds2' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/4d objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/4d/3bb9850b64b025048e726f4b672fd909e23de3.debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7d objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7d/0a4c597d607441446caf09ed67e29ac8b41aab.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7d/0a4c597d607441446caf09ed67e29ac8b41aab.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7d/0a4c597d607441446caf09ed67e29ac8b41aab.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/9e objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/9e/fbd43ccca6571197727d0765f0b40e750c4242.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/9e/fbd43ccca6571197727d0765f0b40e750c4242.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/9e/fbd43ccca6571197727d0765f0b40e750c4242.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/28 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/28/57c01a514993f539cffd84093393669d7df007.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/28/57c01a514993f539cffd84093393669d7df007.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/28/57c01a514993f539cffd84093393669d7df007.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5e objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5e/d6b0bfc3c95e66aa3d0b402fec47297aa51865.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5e/d6b0bfc3c95e66aa3d0b402fec47297aa51865.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/5e/d6b0bfc3c95e66aa3d0b402fec47297aa51865.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c4 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c4/dcf3656aecac595d3bd7b5b44409ca4b4d89fe.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c4/dcf3656aecac595d3bd7b5b44409ca4b4d89fe.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c4/dcf3656aecac595d3bd7b5b44409ca4b4d89fe.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/libhts3t64/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/libhts3t64/usr/lib/debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc ln -s libhts3t64 debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc/libhts3t64-dbgsym install -m0755 -d debian/.debhelper/libhts3t64 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/4d/3bb9850b64b025048e726f4b672fd909e23de3.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/4d/3bb9850b64b025048e726f4b672fd909e23de3.debug debian/tabix/usr/bin/tabix install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2b objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2b/6fe061e9fa31bffd4589ff2b129afaaee9be3f.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2b/6fe061e9fa31bffd4589ff2b129afaaee9be3f.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2b/6fe061e9fa31bffd4589ff2b129afaaee9be3f.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2a objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2a/509b35bde8993f918039e5a51fdf4efb42c64d.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2a/509b35bde8993f918039e5a51fdf4efb42c64d.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2a/509b35bde8993f918039e5a51fdf4efb42c64d.debug debian/tabix/usr/bin/htsfile install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym install -m0755 -d debian/.debhelper/tabix make[1]: Leaving directory '/build/reproducible-path/htslib-1.22.1+ds2' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.22.1+ds2)" >> debian/libhts3t64/DEBIAN/shlibs chmod 0644 -- debian/libhts3t64/DEBIAN/shlibs dpkg-gensymbols -plibhts3t64 -Idebian/libhts3t64.symbols -Pdebian/libhts3t64 -edebian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 mv debian/.debhelper/generated/libhts3t64/triggers.new debian/.debhelper/generated/libhts3t64/triggers mv debian/libhts3t64.substvars.new debian/libhts3t64.substvars rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.22.1 debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so dh_installdeb install -m0755 -d debian/libhts3t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3t64/triggers debian/libhts3t64/DEBIAN/triggers install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN dh_gencontrol install -m0755 -d debian/libhts-dev/DEBIAN echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -cdebian/control -Pdebian/libhts-dev install -m0755 -d debian/libhts3t64/DEBIAN echo misc:Depends= >> debian/libhts3t64.substvars echo misc:Pre-Depends= >> debian/libhts3t64.substvars install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/.debhelper/libhts3t64/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libhts3t64-dbgsym "-DDepends=libhts3t64 (= \${binary:Version})" "-DDescription=debug symbols for libhts3t64" "-DBuild-Ids=2857c01a514993f539cffd84093393669d7df007 5ed6b0bfc3c95e66aa3d0b402fec47297aa51865 7d0a4c597d607441446caf09ed67e29ac8b41aab 9efbd43ccca6571197727d0765f0b40e750c4242 c4dcf3656aecac595d3bd7b5b44409ca4b4d89fe" -DSection=debug -UReplaces -UBreaks install -m0755 -d debian/htslib-test/DEBIAN echo misc:Depends= >> debian/htslib-test.substvars echo misc:Pre-Depends= >> debian/htslib-test.substvars dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -cdebian/control -Pdebian/htslib-test install -m0755 -d debian/tabix/DEBIAN echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=2a509b35bde8993f918039e5a51fdf4efb42c64d 2b6fe061e9fa31bffd4589ff2b129afaaee9be3f 4d3bb9850b64b025048e726f4b672fd909e23de3" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/libhts3t64 chmod 0644 -- debian/libhts-dev/DEBIAN/control chmod 0644 -- debian/htslib-test/DEBIAN/control chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/tabix chmod 0644 -- debian/libhts3t64/DEBIAN/control chmod 0644 -- debian/tabix/DEBIAN/control dh_md5sums install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/libhts3t64/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN chmod 0644 -- debian/libhts3t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/libhts3t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root .. dpkg-deb --root-owner-group --build debian/libhts3t64 .. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb: building package 'libhts3t64-dbgsym' in '../libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb'. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.22.1+ds2-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.22.1+ds2-1_amd64.deb'. dpkg-deb: building package 'tabix' in '../tabix_1.22.1+ds2-1_amd64.deb'. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.22.1+ds2-1_amd64.deb'. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.22.1+ds2-1_all.deb'. dpkg-genbuildinfo --build=binary -O../htslib_1.22.1+ds2-1_amd64.buildinfo dpkg-genchanges --build=binary -O../htslib_1.22.1+ds2-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from htslib-1.22.1+ds2/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full 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/11543 and its subdirectories I: Current time: Sun Sep 7 12:17:34 -12 2025 I: pbuilder-time-stamp: 1757290654 Mon Sep 8 00:17:35 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon Sep 8 00:17:35 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon Sep 8 00:23:23 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon Sep 8 00:23:23 UTC 2025 I: htslib_1.22.1+ds2-1_amd64.changes: Format: 1.8 Date: Thu, 04 Sep 2025 13:56:30 +0200 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: all amd64 Version: 1.22.1+ds2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: htslib-test - Test data for HTSlib libhts-dev - development files for the HTSlib libhts3t64 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.22.1+ds2-1) unstable; urgency=medium . * Properly clean the upstream release tarball. * Don't ship architecture-specific files in htslib-test; regenerate them at test-time using autoconf. * d/libhts3t64.symbols: add new symbols for the latest release. Checksums-Sha1: 84141884967e05145574a01995d790345c1d1cbc 1226576 htslib-test_1.22.1+ds2-1_all.deb 68bc61ea30d4e534d964277b6fc768025d042dd7 8049 htslib_1.22.1+ds2-1_amd64.buildinfo f8daa8f4924b7ed807cdb65fdb718ce3f499d2dc 1778244 libhts-dev_1.22.1+ds2-1_amd64.deb 9a81ae7287a81321b585bcec2b0f68555efc0076 1345216 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb dc83c05999ac1c5f37ff5f6b2f6a290889425c8d 474168 libhts3t64_1.22.1+ds2-1_amd64.deb dd0702d61adc5154eaef3b77d0b8927c252fd569 3111644 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 8dd6f2b7bea51ca80c94e27f3f0988a37e956edb 506760 tabix_1.22.1+ds2-1_amd64.deb Checksums-Sha256: 5e2df11a4c99c05f08883ffe8ac4606e7bc2eb866f19824a05e2bce8809edb5e 1226576 htslib-test_1.22.1+ds2-1_all.deb 3ff2e507b5a949677ff2df0f06ab618ab38b66b78845062485727ba7ec14cb0e 8049 htslib_1.22.1+ds2-1_amd64.buildinfo 21b35960adf1446c99069936c8bae983b79907e061b8e1685913f0dfb43cd2da 1778244 libhts-dev_1.22.1+ds2-1_amd64.deb 03df6251576de1786962a922d7ce208cd347c80511182c1e3283b0911c105e23 1345216 libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb a7eb43ecd83f4fb55c1b8abffb56994cc0e9605f4fb66d64b7c3a9769ff67e69 474168 libhts3t64_1.22.1+ds2-1_amd64.deb e92fca10022b0ebbb9647afcccd48e12124dd2937edd5b54b8ac46611d803bae 3111644 tabix-dbgsym_1.22.1+ds2-1_amd64.deb 9ecd1e8914778fea85e13e7a7a90d4041df16fc07ac60d1e10e868f560331831 506760 tabix_1.22.1+ds2-1_amd64.deb Files: 1238f8072012c5ba07629541f6e1c958 1226576 science optional htslib-test_1.22.1+ds2-1_all.deb 36ea7729c127cec50aaa86ff86c4d027 8049 science optional htslib_1.22.1+ds2-1_amd64.buildinfo 2d3681db05c44e95b7fb05ce2c6bba69 1778244 libdevel optional libhts-dev_1.22.1+ds2-1_amd64.deb 1c8eb72a4df34c6f3929b38926b579d2 1345216 debug optional libhts3t64-dbgsym_1.22.1+ds2-1_amd64.deb 67a22410f672f42da3d5060bf22765af 474168 libs optional libhts3t64_1.22.1+ds2-1_amd64.deb 54304f659cf6319c0a732c3d206ae9bf 3111644 debug optional tabix-dbgsym_1.22.1+ds2-1_amd64.deb 2126774f7e31ff3249f92938705efb2a 506760 science optional tabix_1.22.1+ds2-1_amd64.deb Mon Sep 8 00:23:24 UTC 2025 I: diffoscope 305 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_31-56735.service; invocation ID: 9e972cc97267494cb9d1ab1c9d02117a # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.11Dssgvs/htslib_1.22.1+ds2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.11Dssgvs/htslib_1.22.1+ds2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.11Dssgvs/htslib_1.22.1+ds2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.11Dssgvs/b1/htslib_1.22.1+ds2-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.11Dssgvs/b2/htslib_1.22.1+ds2-1_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: 207ms CPU time consumed: 179ms Memory peak: 18.1M (swap: 0B) Mon Sep 8 00:27:18 UTC 2025 I: diffoscope 305 found no differences in the changes files, and a .buildinfo file also exists. Mon Sep 8 00:27:18 UTC 2025 I: htslib from forky built successfully and reproducibly on amd64. Mon Sep 8 00:27:19 UTC 2025 I: Removing signed htslib_1.22.1+ds2-1_amd64.buildinfo.asc files: removed './b1/htslib_1.22.1+ds2-1_amd64.buildinfo.asc' removed './b2/htslib_1.22.1+ds2-1_amd64.buildinfo.asc'