Thu Jun 1 17:49:54 UTC 2023 I: starting to build staden-io-lib/bookworm/i386 on jenkins on '2023-06-01 17:49'
Thu Jun 1 17:49:54 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_10/96/console.log
Thu Jun 1 17:49:54 UTC 2023 I: Downloading source for bookworm/staden-io-lib=1.14.15-1
--2023-06-01 17:49:55-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/staden-io-lib/staden-io-lib_1.14.15-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2519 (2.5K) [text/prs.lines.tag]
Saving to: ‘staden-io-lib_1.14.15-1.dsc’
0K .. 100% 202M=0s
2023-06-01 17:49:55 (202 MB/s) - ‘staden-io-lib_1.14.15-1.dsc’ saved [2519/2519]
Thu Jun 1 17:49:55 UTC 2023 I: staden-io-lib_1.14.15-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: staden-io-lib
Binary: staden-io-lib-utils, libstaden-read-dev, libstaden-read14, staden-io-lib-examples
Architecture: any all
Version: 1.14.15-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Thorsten Alteholz <debian@alteholz.de>, Michael R. Crusoe <crusoe@debian.org>
Homepage: https://github.com/jkbonfield/io_lib
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/staden-io-lib
Vcs-Git: https://salsa.debian.org/med-team/staden-io-lib.git
Testsuite: autopkgtest
Testsuite-Triggers: smalt-examples
Build-Depends: debhelper-compat (= 13), zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, libhtscodecs-dev, d-shlibs, libbz2-dev, liblzma-dev
Package-List:
libstaden-read-dev deb libdevel optional arch=any
libstaden-read14 deb libs optional arch=any
staden-io-lib-examples deb science optional arch=all
staden-io-lib-utils deb science optional arch=any
Checksums-Sha1:
9008d09e7a06f69b075fbbf3ea08182ea00ba798 3382074 staden-io-lib_1.14.15.orig.tar.gz
2beae21a017d2c156798ee4636ab3d1c0453fc6a 16740 staden-io-lib_1.14.15-1.debian.tar.xz
Checksums-Sha256:
4444c78846e49a493ff09d56d55ebe61140bb0a76ec5fa1c27eff13ec9dabd8b 3382074 staden-io-lib_1.14.15.orig.tar.gz
b8146de2beaac3c8022340ced5f23355551e5c98d42b4fb331d071095551664f 16740 staden-io-lib_1.14.15-1.debian.tar.xz
Files:
1854e7662c06ae93d9037719b9421d70 3382074 staden-io-lib_1.14.15.orig.tar.gz
b17d6f85d5b735ed22f06f343d147b30 16740 staden-io-lib_1.14.15-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=aNY4
-----END PGP SIGNATURE-----
Thu Jun 1 17:49:55 UTC 2023 I: Checking whether the package is not for us
Thu Jun 1 17:49:55 UTC 2023 I: Starting 1st build on remote node ionos6-i386.debian.net.
Thu Jun 1 17:49:55 UTC 2023 I: Preparing to do remote build '1' on ionos6-i386.debian.net.
Thu Jun 1 17:55:39 UTC 2023 I: Deleting $TMPDIR on ionos6-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Wed Jul 3 12:12:57 -12 2024
I: pbuilder-time-stamp: 1720051977
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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: using eatmydata during job
I: Copying source file
I: copying [staden-io-lib_1.14.15-1.dsc]
I: copying [./staden-io-lib_1.14.15.orig.tar.gz]
I: copying [./staden-io-lib_1.14.15-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Mon Mar 13 19:04:22 2023 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./staden-io-lib_1.14.15-1.dsc: no acceptable signature found
dpkg-source: info: extracting staden-io-lib in staden-io-lib-1.14.15
dpkg-source: info: unpacking staden-io-lib_1.14.15.orig.tar.gz
dpkg-source: info: unpacking staden-io-lib_1.14.15-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying pathmax.patch
dpkg-source: info: applying fix_fseeko.patch
dpkg-source: info: applying usedebianhtscodecs.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/130031/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='4588c2f60948404fa710de6ddfc52a8d'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='130031'
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.HrCAmrxX/pbuilderrc_sdCm --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HrCAmrxX/b1 --logfile b1/build.log staden-io-lib_1.14.15-1.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos6-i386 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 2023 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 2023 more
-rwsr-xr-x 1 root root 58912 Mar 22 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/130031/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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: debhelper-compat (= 13), zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, libhtscodecs-dev, d-shlibs, libbz2-dev, liblzma-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19599 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-nss-dev; however:
Package libcurl4-gnutls-dev is not installed.
Package libcurl4-nss-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhtscodecs-dev; however:
Package libhtscodecs-dev is not installed.
pbuilder-satisfydepends-dummy depends on d-shlibs; however:
Package d-shlibs is not installed.
pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
Package libbz2-dev is not installed.
pbuilder-satisfydepends-dummy depends on liblzma-dev; however:
Package liblzma-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget
0 packages upgraded, 46 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.0 MB of archives. After unpacking 84.5 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 d-shlibs all 0.104 [18.6 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libbz2-dev i386 1.0.8-5+b1 [31.5 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-10 [413 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-10 [527 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 libhtscodecs-dev i386 1.3.0-4 [2846 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Fetched 25.0 MB in 0s (59.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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 ... 19599 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_i386.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ...
Unpacking libmagic1:i386 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ...
Unpacking libuchardet0:i386 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_i386.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package d-shlibs.
Preparing to unpack .../15-d-shlibs_0.104_all.deb ...
Unpacking d-shlibs (0.104) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:i386.
Preparing to unpack .../23-libelf1_0.188-2.1_i386.deb ...
Unpacking libelf1:i386 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.15-1_i386.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../25-libicu72_72.1-3_i386.deb ...
Unpacking libicu72:i386 (72.1-3) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.2_i386.deb ...
Unpacking libxml2:i386 (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.21-12_i386.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package libbrotli1:i386.
Preparing to unpack .../31-libbrotli1_1.0.9-2+b6_i386.deb ...
Unpacking libbrotli1:i386 (1.0.9-2+b6) ...
Selecting previously unselected package libbz2-dev:i386.
Preparing to unpack .../32-libbz2-dev_1.0.8-5+b1_i386.deb ...
Unpacking libbz2-dev:i386 (1.0.8-5+b1) ...
Selecting previously unselected package libsasl2-modules-db:i386.
Preparing to unpack .../33-libsasl2-modules-db_2.1.28+dfsg-10_i386.deb ...
Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg-10) ...
Selecting previously unselected package libsasl2-2:i386.
Preparing to unpack .../34-libsasl2-2_2.1.28+dfsg-10_i386.deb ...
Unpacking libsasl2-2:i386 (2.1.28+dfsg-10) ...
Selecting previously unselected package libldap-2.5-0:i386.
Preparing to unpack .../35-libldap-2.5-0_2.5.13+dfsg-5_i386.deb ...
Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5) ...
Selecting previously unselected package libnghttp2-14:i386.
Preparing to unpack .../36-libnghttp2-14_1.52.0-1_i386.deb ...
Unpacking libnghttp2-14:i386 (1.52.0-1) ...
Selecting previously unselected package libpsl5:i386.
Preparing to unpack .../37-libpsl5_0.21.2-1_i386.deb ...
Unpacking libpsl5:i386 (0.21.2-1) ...
Selecting previously unselected package librtmp1:i386.
Preparing to unpack .../38-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ...
Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:i386.
Preparing to unpack .../39-libssh2-1_1.10.0-3+b1_i386.deb ...
Unpacking libssh2-1:i386 (1.10.0-3+b1) ...
Selecting previously unselected package libcurl3-gnutls:i386.
Preparing to unpack .../40-libcurl3-gnutls_7.88.1-10_i386.deb ...
Unpacking libcurl3-gnutls:i386 (7.88.1-10) ...
Selecting previously unselected package libcurl4-gnutls-dev:i386.
Preparing to unpack .../41-libcurl4-gnutls-dev_7.88.1-10_i386.deb ...
Unpacking libcurl4-gnutls-dev:i386 (7.88.1-10) ...
Selecting previously unselected package libhtscodecs2:i386.
Preparing to unpack .../42-libhtscodecs2_1.3.0-4_i386.deb ...
Unpacking libhtscodecs2:i386 (1.3.0-4) ...
Selecting previously unselected package libhtscodecs-dev:i386.
Preparing to unpack .../43-libhtscodecs-dev_1.3.0-4_i386.deb ...
Unpacking libhtscodecs-dev:i386 (1.3.0-4) ...
Selecting previously unselected package liblzma-dev:i386.
Preparing to unpack .../44-liblzma-dev_5.4.1-0.2_i386.deb ...
Unpacking liblzma-dev:i386 (5.4.1-0.2) ...
Selecting previously unselected package zlib1g-dev:i386.
Preparing to unpack .../45-zlib1g-dev_1%3a1.2.13.dfsg-1_i386.deb ...
Unpacking zlib1g-dev:i386 (1:1.2.13.dfsg-1) ...
Setting up libhtscodecs2:i386 (1.3.0-4) ...
Setting up libpipeline1:i386 (1.5.7-1) ...
Setting up libpsl5:i386 (0.21.2-1) ...
Setting up libicu72:i386 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libbrotli1:i386 (1.0.9-2+b6) ...
Setting up libnghttp2-14:i386 (1.52.0-1) ...
Setting up libmagic1:i386 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ...
Setting up libhtscodecs-dev:i386 (1.3.0-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up autopoint (0.21-12) ...
Setting up d-shlibs (0.104) ...
Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ...
Setting up autoconf (2.71-3) ...
Setting up liblzma-dev:i386 (5.4.1-0.2) ...
Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:i386 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:i386 (1.10.0-3+b1) ...
Setting up libelf1:i386 (0.188-2.1) ...
Setting up libxml2:i386 (2.9.14+dfsg-1.2) ...
Setting up libbz2-dev:i386 (1.0.8-5+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libcurl3-gnutls:i386 (7.88.1-10) ...
Setting up libcurl4-gnutls-dev:i386 (7.88.1-10) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.4) ...
Processing triggers for libc-bin (2.36-9) ...
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/staden-io-lib-1.14.15/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../staden-io-lib_1.14.15-1_source.changes
dpkg-buildpackage: info: source package staden-io-lib
dpkg-buildpackage: info: source version 1.14.15-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --no-parallel
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
dh_auto_clean
rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam
rm -f config.sub config.guess
##
## Try to verify correct ABI version right in the beginning
## Strangely enough d-shlibmove fails in detecting it in this package
## Since upstream build system creates libstaden-read.so.11.1.0 this code is not
## activated but it should be considered in case of future problems with ABI version
##
#UPSTREAMABI=`grep ^VERS_CURRENT configure.in | sed 's/^VERS_CURRENT[[:space:]]*=\([0-9]\+\)[[:space:]]*/\1/'` ; \
#DEBABI=`grep '^Package: libstaden-read[0-9]\+' debian/control | sed 's/Package: libstaden-read\([0-9]\+\)/\1/'` ; \
#if [ ${UPSTREAMABI} -ne ${DEBABI} ] ; then \
# echo "Upstream has bumped ABI to ${UPSTREAMABI} but Debian is using libstaden-read${DEBABI} (see bug #710225)" ; \
# exit 1 ; \
#fi
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
dh_autoreconf_clean -O--no-parallel
dh_clean -O--no-parallel
debian/rules binary
dh binary --no-parallel
dh_update_autotools_config -O--no-parallel
dh_autoreconf -O--no-parallel
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:81: warning: The macro `AC_PROG_LIBTOOL' is obsolete.
configure.ac:81: You should run autoupdate.
m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from...
configure.ac:81: the top level
configure.ac:101: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:101: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from...
configure.ac:101: the top level
configure.ac:102: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:102: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from...
configure.ac:102: the top level
configure.ac:102: warning: The macro `AC_LANG_C' is obsolete.
configure.ac:102: You should run autoupdate.
./lib/autoconf/c.m4:72: AC_LANG_C is expanded from...
acinclude.m4:281: ZLIB_CHECK_CONFIG is expanded from...
configure.ac:102: the top level
configure.ac:156: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:156: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
m4/ax_with_libdeflate.m4:31: AX_LIBDEFLATE is expanded from...
configure.ac:156: the top level
configure.ac:157: warning: The macro `AC_HELP_STRING' is obsolete.
configure.ac:157: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
m4/ax_with_zstd.m4:31: AX_ZSTD is expanded from...
configure.ac:157: the top level
configure.ac:190: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:190: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:190: the top level
configure.ac:255: warning: AC_OUTPUT should be used without arguments.
configure.ac:255: You should run autoupdate.
configure.ac:79: installing './compile'
configure.ac:81: installing './config.guess'
configure.ac:81: installing './config.sub'
configure.ac:10: installing './install-sh'
configure.ac:10: installing './missing'
io_lib/Makefile.am: installing './depcomp'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
export ac_cv_func_mmap_fixed_mapped=yes && dh_auto_configure
./configure --build=i686-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/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/param.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for grep that handles long lines and -e... (cached) /bin/grep
checking for C compiler warning flags... -Wall
checking for gawk... (cached) mawk
checking for curl-config... /usr/bin/curl-config
checking for the version of libcurl... 7.88.1
checking whether libcurl just needs -lcurl... yes
checking whether libcurl is usable... yes
checking for curl_free... yes
checking for inflateEnd in -lz... yes
checking for zlib.h... yes
checking for library containing gethostbyname... none required
checking for library containing socket... none required
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for bsc_compress in -lbsc... no
checking whether byte ordering is bigendian... no
checking for egrep... (cached) /bin/grep -E
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for fcntl.h... yes
checking for limits.h... yes
checking for unistd.h... (cached) yes
checking for malloc.h... yes
checking for zlib.h... (cached) yes
checking for stdio_ext.h... yes
checking whether byte ordering is bigendian... (cached) no
checking size of short... 2
checking size of int... 4
checking size of long... 4
checking for inline... inline
checking for mode_t... yes
checking for fileno... yes
checking for fstat... yes
checking for mallopt... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for getpagesize... yes
checking for working mmap... (cached) yes
checking for library containing pthread_join... none required
checking for library containing cos... -lm
checking for strdup... yes
checking for fsync... yes
checking that generated files are newer than configure... done
=== configuring in htscodecs (/build/staden-io-lib-1.14.15/htscodecs)
configure: WARNING: no configuration information is in htscodecs
configure: creating ./config.status
config.status: creating Makefile
config.status: creating io_lib/Makefile
config.status: creating progs/Makefile
config.status: creating tests/Makefile
config.status: creating io_lib-config
config.status: creating io_lib/os.h
config.status: creating io_lib/version.h
config.status: creating io_lib_config.h
config.status: executing depfiles commands
config.status: executing libtool commands
--------------------------------------------------
CONFIGURE SUMMARY
--------------------------------------------------
Bzip2 enabled: yes
lzma enabled: yes
custom-buffering enabled: yes
Using own crc: yes
Libcurl enabled: yes
Libdeflate enabled: no
have libbsc: no
Have zstd: no
CC: gcc
CFLAGS: -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security
LDFLAGS: -Wl,-z,relro -Wl,-z,now
LIBS: -lm -llzma -lbz2
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
dh_auto_build -O--no-parallel
make -j1
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
make all-recursive
make[2]: Entering directory '/build/staden-io-lib-1.14.15'
Making all in io_lib
make[3]: Entering directory '/build/staden-io-lib-1.14.15/io_lib'
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c Read.c -o libstaden_read_la-Read.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c scf_extras.c -o libstaden_read_la-scf_extras.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c translate.c -fPIC -DPIC -o .libs/libstaden_read_la-translate.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c translate.c -o libstaden_read_la-translate.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c compression.c -o libstaden_read_la-compression.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr.c -o libstaden_read_la-ztr.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c ztr_translate.c -o libstaden_read_la-ztr_translate.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c deflate_interlaced.c -o libstaden_read_la-deflate_interlaced.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c fpoint.c -fPIC -DPIC -o .libs/libstaden_read_la-fpoint.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c fpoint.c -o libstaden_read_la-fpoint.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOABI.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOABI.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOABI.c -o libstaden_read_la-seqIOABI.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c expFileIO.c -fPIC -DPIC -o .libs/libstaden_read_la-expFileIO.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c expFileIO.c -o libstaden_read_la-expFileIO.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOPlain.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOPlain.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c seqIOPlain.c -o libstaden_read_la-seqIOPlain.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-misc_scf.lo `test -f 'misc_scf.c' || echo './'`misc_scf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-misc_scf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c misc_scf.c -o libstaden_read_la-misc_scf.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-read_scf.lo `test -f 'read_scf.c' || echo './'`read_scf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c read_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-read_scf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c read_scf.c -o libstaden_read_la-read_scf.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-write_scf.lo `test -f 'write_scf.c' || echo './'`write_scf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c write_scf.c -fPIC -DPIC -o .libs/libstaden_read_la-write_scf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c write_scf.c -o libstaden_read_la-write_scf.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c sff.c -fPIC -DPIC -o .libs/libstaden_read_la-sff.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c sff.c -o libstaden_read_la-sff.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c srf.c -fPIC -DPIC -o .libs/libstaden_read_la-srf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c srf.c -o libstaden_read_la-srf.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-array.lo `test -f 'array.c' || echo './'`array.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c array.c -fPIC -DPIC -o .libs/libstaden_read_la-array.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c array.c -o libstaden_read_la-array.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-compress.lo `test -f 'compress.c' || echo './'`compress.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c compress.c -fPIC -DPIC -o .libs/libstaden_read_la-compress.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c compress.c -o libstaden_read_la-compress.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-error.lo `test -f 'error.c' || echo './'`error.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c error.c -fPIC -DPIC -o .libs/libstaden_read_la-error.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c error.c -o libstaden_read_la-error.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-files.lo `test -f 'files.c' || echo './'`files.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c files.c -fPIC -DPIC -o .libs/libstaden_read_la-files.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c files.c -o libstaden_read_la-files.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-find.lo `test -f 'find.c' || echo './'`find.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c find.c -fPIC -DPIC -o .libs/libstaden_read_la-find.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c find.c -o libstaden_read_la-find.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-mach-io.lo `test -f 'mach-io.c' || echo './'`mach-io.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c mach-io.c -fPIC -DPIC -o .libs/libstaden_read_la-mach-io.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c mach-io.c -o libstaden_read_la-mach-io.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-open_trace_file.lo `test -f 'open_trace_file.c' || echo './'`open_trace_file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c open_trace_file.c -fPIC -DPIC -o .libs/libstaden_read_la-open_trace_file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c open_trace_file.c -o libstaden_read_la-open_trace_file.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-read_alloc.lo `test -f 'read_alloc.c' || echo './'`read_alloc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c read_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-read_alloc.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c read_alloc.c -o libstaden_read_la-read_alloc.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-strings.lo `test -f 'strings.c' || echo './'`strings.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c strings.c -fPIC -DPIC -o .libs/libstaden_read_la-strings.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c strings.c -o libstaden_read_la-strings.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c traceType.c -fPIC -DPIC -o .libs/libstaden_read_la-traceType.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-xalloc.lo `test -f 'xalloc.c' || echo './'`xalloc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c xalloc.c -fPIC -DPIC -o .libs/libstaden_read_la-xalloc.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c xalloc.c -o libstaden_read_la-xalloc.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c vlen.c -fPIC -DPIC -o .libs/libstaden_read_la-vlen.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c hash_table.c -fPIC -DPIC -o .libs/libstaden_read_la-hash_table.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c jenkins_lookup3.c -fPIC -DPIC -o .libs/libstaden_read_la-jenkins_lookup3.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c string_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-string_alloc.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c string_alloc.c -o libstaden_read_la-string_alloc.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 15:2:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/i386-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -llzma -lbz2
libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -lcurl -lhtscodecs -lm -llzma -lbz2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libstaden-read.so.14 -o .libs/libstaden-read.so.14.1.2
libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.2" "libstaden-read.so.14")
libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.2" "libstaden-read.so")
libtool: link: ar cr .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o
libtool: link: ranlib .libs/libstaden-read.a
libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" )
make[3]: Leaving directory '/build/staden-io-lib-1.14.15/io_lib'
Making all in progs
make[3]: Entering directory '/build/staden-io-lib-1.14.15/progs'
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o convert_trace.o convert_trace.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeSCF.o makeSCF.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extract_seq.o extract_seq.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_seq extract_seq.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extract_qual.o extract_qual.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extract_fastq.o extract_fastq.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/extract_fastq extract_fastq.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o index_tar.o index_tar.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o index_tar index_tar.o -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o index_tar index_tar.o -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scf_dump.o scf_dump.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scf_dump scf_dump.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scf_info.o scf_info.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scf_info scf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scf_info scf_info.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scf_update.o scf_update.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scf_update scf_update.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scf_update scf_update.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_comment.o get_comment.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o get_comment get_comment.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/get_comment get_comment.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_tar.o hash_tar.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/hash_tar hash_tar.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_extract.o hash_extract.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/hash_extract hash_extract.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_list.o hash_list.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o hash_list hash_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/hash_list hash_list.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o trace_dump.o trace_dump.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/trace_dump trace_dump.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_sff.o hash_sff.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/hash_sff hash_sff.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o append_sff.o append_sff.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o append_sff append_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/append_sff append_sff.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ztr_dump.o ztr_dump.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/ztr_dump ztr_dump.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_dump_all.o srf_dump_all.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_dump_all srf_dump_all.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_index_hash.o srf_index_hash.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_index_hash srf_index_hash.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_extract_linear.o srf_extract_linear.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_extract_linear srf_extract_linear.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_extract_hash.o srf_extract_hash.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_extract_hash srf_extract_hash.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf2fastq.o srf2fastq.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf2fastq srf2fastq.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf2fasta.o srf2fasta.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf2fasta srf2fasta.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_filter.o srf_filter.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_info.o srf_info.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_info srf_info.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_list.o srf_list.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/srf_list srf_list.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_exp.o hash_exp.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_dump.o cram_dump.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_index.o cram_index.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scramble.o scramble.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_merge.o scram_merge.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_pileup.o scram_pileup.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_flagstat.o scram_flagstat.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scram_test.o scram_test.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_size.o cram_size.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_filter.o cram_filter.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
make[3]: Leaving directory '/build/staden-io-lib-1.14.15/progs'
Making all in tests
make[3]: Entering directory '/build/staden-io-lib-1.14.15/tests'
gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cram_io_test.o cram_io_test.c
/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2
libtool: link: gcc -Wall -g -O2 -ffile-prefix-map=/build/staden-io-lib-1.14.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -lm -llzma -lbz2
make[3]: Leaving directory '/build/staden-io-lib-1.14.15/tests'
make[3]: Entering directory '/build/staden-io-lib-1.14.15'
make[3]: Leaving directory '/build/staden-io-lib-1.14.15'
make[2]: Leaving directory '/build/staden-io-lib-1.14.15'
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
debian/rules override_dh_auto_test-indep
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
echo "Do not run test suite for architecture independent builds"
Do not run test suite for architecture independent builds
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
dh_auto_test -O--no-parallel -Nstaden-io-lib-examples
make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
Making check in io_lib
make[2]: Entering directory '/build/staden-io-lib-1.14.15/io_lib'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/staden-io-lib-1.14.15/io_lib'
Making check in progs
make[2]: Entering directory '/build/staden-io-lib-1.14.15/progs'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/staden-io-lib-1.14.15/progs'
Making check in tests
make[2]: Entering directory '/build/staden-io-lib-1.14.15/tests'
make check-TESTS
make[3]: Entering directory '/build/staden-io-lib-1.14.15/tests'
PASS: srf2fasta.test
PASS: srf2fastq.test
PASS: srf_info.test
Reading archive ./data/both.srf.
PASS: srf_filter.test
NB: The next line is expected to be an error message
Malformed or missing index hash. Consider running srf_index_hash
Nbuckets = 16
Nused = 20
Avg chain = 1.250000
Chain var.= 0.812500
%age full = 81.250000
max len = 3
Chain 0 = 3
Chain 1 = 8
Chain 2 = 3
Chain 3 = 2
PASS: srf_index.test
Loading ce.fa
Generating ce#sorted.sam
Generating ce#unsorted.sam
=== testing ./data/c1#bounds.sam ===
../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam
../progs/scramble -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
../progs/scramble -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
=== testing ./data/c1#clip.sam ===
../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam
../progs/scramble -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
../progs/scramble -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
=== testing ./data/c1#pad1.sam ===
../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam
../progs/scramble -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
../progs/scramble -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
=== testing ./data/c1#pad2.sam ===
../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam
../progs/scramble -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
../progs/scramble -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
=== testing ./data/c1#pad3.sam ===
../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam
../progs/scramble -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
../progs/scramble -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
=== testing ./data/ce#1.sam ===
../progs/scramble ./data/ce#1.sam test.out/ce#1.bam
../progs/scramble -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble test.out/ce#1.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
../progs/scramble -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
=== testing ./data/ce#2.sam ===
../progs/scramble ./data/ce#2.sam test.out/ce#2.bam
../progs/scramble -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble test.out/ce#2.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
../progs/scramble -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
=== testing ./data/ce#5.sam ===
../progs/scramble ./data/ce#5.sam test.out/ce#5.bam
../progs/scramble -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble test.out/ce#5.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
../progs/scramble -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
=== testing ./data/ce#5b.sam ===
../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam
../progs/scramble -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
../progs/scramble -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
=== testing ./data/ce#large_seq.sam ===
../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam
../progs/scramble -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
../progs/scramble -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
=== testing ./data/ce#sorted.sam ===
../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam
../progs/scramble -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
../progs/scramble -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
=== testing ./data/ce#tag_depadded.sam ===
../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
../progs/scramble -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
../progs/scramble -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
=== testing ./data/ce#tag_padded.sam ===
../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
../progs/scramble -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
../progs/scramble -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
=== testing ./data/ce#unmap.sam ===
../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam
../progs/scramble -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
../progs/scramble -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
=== testing ./data/ce#unmap1.sam ===
../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam
../progs/scramble -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
../progs/scramble -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
=== testing ./data/ce#unmap2.sam ===
../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam
../progs/scramble -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
../progs/scramble -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
=== testing ./data/ce#unsorted.sam ===
../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam
../progs/scramble -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
Unsorted mode enabled
../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
../progs/scramble -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
../progs/scramble -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
Unsorted mode enabled
../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
=== testing ./data/tag_aux#aux.sam ===
../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
../progs/scramble -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
=== testing ./data/tag_aux#special.sam ===
../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam
../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
../progs/scramble -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
=== testing ./data/tag_aux#values1.bam ===
../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
../progs/scramble -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
=== testing ./data/tag_aux#values2.bam ===
../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
../progs/scramble -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
=== testing ./data/tag_aux#values4.bam ===
../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
../progs/scramble -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
=== testing ./data/xx#MD.sam ===
../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam
../progs/scramble -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
../progs/scramble -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
=== testing ./data/xx#MD2.sam ===
../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam
../progs/scramble -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
../progs/scramble -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
=== testing ./data/xx#blank.sam ===
../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam
../progs/scramble -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
../progs/scramble -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
=== testing ./data/xx#large_aux.sam ===
../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam
../progs/scramble -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
../progs/scramble -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
=== testing ./data/xx#large_aux2.sam ===
../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
../progs/scramble -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
../progs/scramble -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
=== testing ./data/xx#minimal.sam ===
../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam
../progs/scramble -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
../progs/scramble -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
=== testing ./data/xx#pair.sam ===
../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam
../progs/scramble -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
../progs/scramble -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
=== testing ./data/xx#repeated.sam ===
../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam
../progs/scramble -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
../progs/scramble -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
=== testing ./data/xx#rg.sam ===
../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam
../progs/scramble -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
../progs/scramble -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
=== testing ./data/xx#triplet.sam ===
../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam
../progs/scramble -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
../progs/scramble -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
=== testing ./data/xx#unsorted.sam ===
../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam
../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
../progs/scramble -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
PASS: scram.test
=== testing ./data/c1#bounds.sam ===
../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam
../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
../progs/scramble -V3.0 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
=== testing ./data/c1#clip.sam ===
../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam
../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
../progs/scramble -V3.0 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
=== testing ./data/c1#pad1.sam ===
../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam
../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
../progs/scramble -V3.0 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
=== testing ./data/c1#pad2.sam ===
../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam
../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
../progs/scramble -V3.0 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
=== testing ./data/c1#pad3.sam ===
../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam
../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam
../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
../progs/scramble -V3.0 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
=== testing ./data/ce#1.sam ===
../progs/scramble ./data/ce#1.sam test.out/ce#1.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble test.out/ce#1.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
=== testing ./data/ce#2.sam ===
../progs/scramble ./data/ce#2.sam test.out/ce#2.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble test.out/ce#2.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
=== testing ./data/ce#5.sam ===
../progs/scramble ./data/ce#5.sam test.out/ce#5.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble test.out/ce#5.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
=== testing ./data/ce#5b.sam ===
../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
=== testing ./data/ce#large_seq.sam ===
../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
=== testing ./data/ce#sorted.sam ===
../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
=== testing ./data/ce#tag_depadded.sam ===
../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
=== testing ./data/ce#tag_padded.sam ===
../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
=== testing ./data/ce#unmap.sam ===
../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
=== testing ./data/ce#unmap1.sam ===
../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
=== testing ./data/ce#unmap2.sam ===
../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
=== testing ./data/ce#unsorted.sam ===
../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam
../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
Unsorted mode enabled
../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam
../progs/scramble -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
../progs/scramble -V3.0 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
Unsorted mode enabled
../progs/scramble test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
=== testing ./data/tag_aux#aux.sam ===
../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
../progs/scramble -V3.0 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
../progs/scramble test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
=== testing ./data/tag_aux#special.sam ===
../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam
../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
../progs/scramble -V3.0 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
../progs/scramble test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
=== testing ./data/tag_aux#values1.bam ===
../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
../progs/scramble -V3.0 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
../progs/scramble test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
=== testing ./data/tag_aux#values2.bam ===
../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
../progs/scramble -V3.0 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
../progs/scramble test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
=== testing ./data/tag_aux#values4.bam ===
../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam
../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
../progs/scramble -V3.0 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
../progs/scramble test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
=== testing ./data/xx#MD.sam ===
../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
=== testing ./data/xx#MD2.sam ===
../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
=== testing ./data/xx#blank.sam ===
../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
=== testing ./data/xx#large_aux.sam ===
../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
=== testing ./data/xx#large_aux2.sam ===
../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
=== testing ./data/xx#minimal.sam ===
../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
=== testing ./data/xx#pair.sam ===
../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
=== testing ./data/xx#repeated.sam ===
../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
=== testing ./data/xx#rg.sam ===
../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
=== testing ./data/xx#triplet.sam ===
../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
=== testing ./data/xx#unsorted.sam ===
../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam
../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam
../progs/scramble -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
../progs/scramble -V3.0 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
../progs/scramble test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
=== testing ./data/c1#bounds.sam ===
../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam
../progs/scramble -t4 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
../progs/scramble -t4 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
=== testing ./data/c1#clip.sam ===
../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam
../progs/scramble -t4 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
../progs/scramble -t4 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
=== testing ./data/c1#pad1.sam ===
../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam
../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
../progs/scramble -t4 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
=== testing ./data/c1#pad2.sam ===
../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam
../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
../progs/scramble -t4 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
=== testing ./data/c1#pad3.sam ===
../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam
../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
../progs/scramble -t4 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
=== testing ./data/ce#1.sam ===
../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
../progs/scramble -t4 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
=== testing ./data/ce#2.sam ===
../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
../progs/scramble -t4 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
=== testing ./data/ce#5.sam ===
../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
../progs/scramble -t4 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
=== testing ./data/ce#5b.sam ===
../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
../progs/scramble -t4 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
=== testing ./data/ce#large_seq.sam ===
../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
../progs/scramble -t4 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
=== testing ./data/ce#sorted.sam ===
../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
../progs/scramble -t4 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
=== testing ./data/ce#tag_depadded.sam ===
../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
../progs/scramble -t4 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
=== testing ./data/ce#tag_padded.sam ===
../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
../progs/scramble -t4 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
=== testing ./data/ce#unmap.sam ===
../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
../progs/scramble -t4 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
=== testing ./data/ce#unmap1.sam ===
../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
../progs/scramble -t4 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
=== testing ./data/ce#unmap2.sam ===
../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
../progs/scramble -t4 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
=== testing ./data/ce#unsorted.sam ===
../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam
../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
Unsorted mode enabled
../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
../progs/scramble -t4 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
Unsorted mode enabled
../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
=== testing ./data/tag_aux#aux.sam ===
../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
../progs/scramble -t4 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
=== testing ./data/tag_aux#special.sam ===
../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam
../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
../progs/scramble -t4 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
=== testing ./data/tag_aux#values1.bam ===
../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
../progs/scramble -t4 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
=== testing ./data/tag_aux#values2.bam ===
../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
../progs/scramble -t4 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
=== testing ./data/tag_aux#values4.bam ===
../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
../progs/scramble -t4 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
=== testing ./data/xx#MD.sam ===
../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
../progs/scramble -t4 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
=== testing ./data/xx#MD2.sam ===
../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
../progs/scramble -t4 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
=== testing ./data/xx#blank.sam ===
../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
../progs/scramble -t4 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
=== testing ./data/xx#large_aux.sam ===
../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
../progs/scramble -t4 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
=== testing ./data/xx#large_aux2.sam ===
../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
../progs/scramble -t4 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
=== testing ./data/xx#minimal.sam ===
../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
../progs/scramble -t4 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
=== testing ./data/xx#pair.sam ===
../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
../progs/scramble -t4 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
=== testing ./data/xx#repeated.sam ===
../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
../progs/scramble -t4 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
=== testing ./data/xx#rg.sam ===
../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
../progs/scramble -t4 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
=== testing ./data/xx#triplet.sam ===
../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
../progs/scramble -t4 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
=== testing ./data/xx#unsorted.sam ===
../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam
../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
PASS: scram_mt30.test
=== testing ./data/c1#bounds.sam ===
../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam
../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
=== testing ./data/c1#clip.sam ===
../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam
../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
=== testing ./data/c1#pad1.sam ===
../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam
../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
=== testing ./data/c1#pad2.sam ===
../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam
../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
=== testing ./data/c1#pad3.sam ===
../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam
../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
=== testing ./data/ce#1.sam ===
../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
=== testing ./data/ce#2.sam ===
../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
=== testing ./data/ce#5.sam ===
../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
=== testing ./data/ce#5b.sam ===
../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
=== testing ./data/ce#large_seq.sam ===
../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
=== testing ./data/ce#sorted.sam ===
../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
=== testing ./data/ce#tag_depadded.sam ===
../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
=== testing ./data/ce#tag_padded.sam ===
../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
=== testing ./data/ce#unmap.sam ===
../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
=== testing ./data/ce#unmap1.sam ===
../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
=== testing ./data/ce#unmap2.sam ===
../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
=== testing ./data/ce#unsorted.sam ===
../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam
../progs/scramble -t4 -V3.1 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Unsorted mode enabled
../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Unsorted mode enabled
../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
=== testing ./data/tag_aux#aux.sam ===
../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
=== testing ./data/tag_aux#special.sam ===
../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam
../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
=== testing ./data/tag_aux#values1.bam ===
../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
=== testing ./data/tag_aux#values2.bam ===
../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
=== testing ./data/tag_aux#values4.bam ===
../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
../progs/scramble -t4 -V3.1 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
=== testing ./data/xx#MD.sam ===
../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
=== testing ./data/xx#MD2.sam ===
../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
=== testing ./data/xx#blank.sam ===
../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
=== testing ./data/xx#large_aux.sam ===
../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
=== testing ./data/xx#large_aux2.sam ===
../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
=== testing ./data/xx#minimal.sam ===
../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
=== testing ./data/xx#pair.sam ===
../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
=== testing ./data/xx#repeated.sam ===
../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
=== testing ./data/xx#rg.sam ===
../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
=== testing ./data/xx#triplet.sam ===
../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -V3.1 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -V3.1 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
=== testing ./data/xx#unsorted.sam ===
../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam
../progs/scramble -t4 -V3.1 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
../progs/scramble -t4 -V3.1 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
../progs/scramble -t4 -V3.1 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
WARNING: this version of CRAM has yet to be formally signed off.
CRAM 3.1 has multiple implementations that have been cross-validated, but
the specification document has not yet been accepted as an official standard.
../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
PASS: scram_mt31.test
=== testing ./data/c1#bounds.sam ===
../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
=== testing ./data/c1#clip.sam ===
../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
=== testing ./data/c1#pad1.sam ===
../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
=== testing ./data/c1#pad2.sam ===
../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
=== testing ./data/c1#pad3.sam ===
../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
=== testing ./data/ce#1.sam ===
../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam
./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
=== testing ./data/ce#2.sam ===
../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam
./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
=== testing ./data/ce#5.sam ===
../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam
./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
=== testing ./data/ce#5b.sam ===
../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
=== testing ./data/ce#large_seq.sam ===
../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
=== testing ./data/ce#sorted.sam ===
../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
=== testing ./data/ce#tag_depadded.sam ===
../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
=== testing ./data/ce#tag_padded.sam ===
../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
=== testing ./data/ce#unmap.sam ===
../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
=== testing ./data/ce#unmap1.sam ===
../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
=== testing ./data/ce#unmap2.sam ===
../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
=== testing ./data/ce#unsorted.sam ===
../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Unsorted mode enabled
../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Unsorted mode enabled
../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
=== testing ./data/tag_aux#aux.sam ===
../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
=== testing ./data/tag_aux#special.sam ===
../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
=== testing ./data/tag_aux#values1.bam ===
../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
=== testing ./data/tag_aux#values2.bam ===
../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
=== testing ./data/tag_aux#values4.bam ===
../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
../progs/scramble -t4 -V4.0 -7 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded reference with non-coordinate sorted data is not supported.
Using -x for no-ref instead.
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Embedded consensus with non-coordinate sorted data is not supported.
../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
=== testing ./data/xx#MD.sam ===
../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
=== testing ./data/xx#MD2.sam ===
../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
=== testing ./data/xx#blank.sam ===
../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
=== testing ./data/xx#large_aux.sam ===
../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
=== testing ./data/xx#large_aux2.sam ===
../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
=== testing ./data/xx#minimal.sam ===
../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
=== testing ./data/xx#pair.sam ===
../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
=== testing ./data/xx#repeated.sam ===
../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
=== testing ./data/xx#rg.sam ===
../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
=== testing ./data/xx#triplet.sam ===
../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
=== testing ./data/xx#unsorted.sam ===
../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam
../progs/scramble -t4 -V4.0 -7 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam
../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
../progs/scramble -t4 -V4.0 -7 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam
./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
../progs/scramble -t4 -V4.0 -7 -x longref.sam test.out/longref.cram
WARNING: this version of CRAM is not a recognised GA4GH standard.
Note this CRAM version is a technology demonstration only.
Future versions of Scramble may not be able to read these files.
Unsorted mode enabled
../progs/scramble -t4 -q test.out/longref.cram test.out/longref.sam
./compare_sam.pl test.out/longref.sam ./data/longref.sam
PASS: scram_mt40.test
PASS: cram_io.test
=== testing ./data/ce#5b_java.cram ===
../progs/scramble -t4 -r ./data/ce.fa ./data/ce#5b_java.cram test.out/ce#5b_java.scramble.sam
./compare_sam.pl ./data/ce#5b_java.sam test.out/ce#5b_java.scramble.sam
=== testing ./data/tag_aux#aux_java.cram ===
../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#aux_java.cram test.out/tag_aux#aux_java.scramble.sam
./compare_sam.pl ./data/tag_aux#aux_java.sam test.out/tag_aux#aux_java.scramble.sam
=== testing ./data/xx#large_aux_java.cram ===
../progs/scramble -t4 -r ./data/xx.fa ./data/xx#large_aux_java.cram test.out/xx#large_aux_java.scramble.sam
./compare_sam.pl ./data/xx#large_aux_java.sam test.out/xx#large_aux_java.scramble.sam
=== testing ./data/9827_rand3.cram ===
../progs/scramble -t4 -r ./data/9827_rand3.cram ./data/9827_rand3.cram test.out/9827_rand3.scramble.sam
./data/9827_rand3.cram.fai: No such file or directory
./compare_sam.pl ./data/9827_rand3.sam test.out/9827_rand3.scramble.sam
PASS: java.test
===================
All 11 tests passed
===================
make[3]: Leaving directory '/build/staden-io-lib-1.14.15/tests'
make[2]: Leaving directory '/build/staden-io-lib-1.14.15/tests'
make[2]: Entering directory '/build/staden-io-lib-1.14.15'
make[2]: Leaving directory '/build/staden-io-lib-1.14.15'
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--no-parallel
dh_prep -O--no-parallel
dh_auto_install -O--no-parallel
make -j1 install DESTDIR=/build/staden-io-lib-1.14.15/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
Making install in io_lib
make[2]: Entering directory '/build/staden-io-lib-1.14.15/io_lib'
make[3]: Entering directory '/build/staden-io-lib-1.14.15/io_lib'
/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu'
/bin/bash ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.2 /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.so.14.1.2
libtool: install: (cd /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libstaden-read.so.14.1.2 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.2 libstaden-read.so.14; }; })
libtool: install: (cd /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libstaden-read.so.14.1.2 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.2 libstaden-read.so; }; })
libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.la
libtool: install: /usr/bin/install -c .libs/libstaden-read.a /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.a
libtool: install: chmod 644 /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.a
libtool: install: ranlib /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.a
libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/staden-io-lib-1.14.15/io_lib'
make[2]: Leaving directory '/build/staden-io-lib-1.14.15/io_lib'
Making install in progs
make[2]: Entering directory '/build/staden-io-lib-1.14.15/progs'
make[3]: Entering directory '/build/staden-io-lib-1.14.15/progs'
/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/staden-io-lib-1.14.15/debian/tmp/usr/bin'
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/convert_trace /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/convert_trace
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/makeSCF /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/makeSCF
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/extract_seq /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/extract_seq
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/extract_qual /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/extract_qual
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/extract_fastq /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/extract_fastq
libtool: install: /usr/bin/install -c index_tar /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/index_tar
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scf_dump /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scf_dump
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scf_info /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scf_info
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scf_update /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scf_update
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/get_comment /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/get_comment
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/hash_tar /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/hash_tar
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/hash_extract /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/hash_extract
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/hash_list /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/hash_list
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/trace_dump /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/trace_dump
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/hash_sff /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/hash_sff
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/append_sff /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/append_sff
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/ztr_dump /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/ztr_dump
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf_dump_all /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf_dump_all
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf_index_hash /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf_index_hash
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf_extract_linear /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf_extract_linear
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf_extract_hash /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf_extract_hash
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf2fastq /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf2fastq
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf2fasta /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf2fasta
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf_filter /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf_filter
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf_info /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf_info
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/srf_list /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/srf_list
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/hash_exp /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/hash_exp
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/cram_dump /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/cram_dump
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/cram_index /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/cram_index
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scramble /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scramble
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scram_merge /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scram_merge
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scram_pileup /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scram_pileup
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scram_flagstat /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scram_flagstat
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/scram_test /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/scram_test
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/cram_size /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/cram_size
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/i386-linux-gnu'
libtool: install: /usr/bin/install -c .libs/cram_filter /build/staden-io-lib-1.14.15/debian/tmp/usr/bin/cram_filter
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/staden-io-lib-1.14.15/progs'
make[2]: Leaving directory '/build/staden-io-lib-1.14.15/progs'
Making install in tests
make[2]: Entering directory '/build/staden-io-lib-1.14.15/tests'
make[3]: Entering directory '/build/staden-io-lib-1.14.15/tests'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/staden-io-lib-1.14.15/tests'
make[2]: Leaving directory '/build/staden-io-lib-1.14.15/tests'
make[2]: Entering directory '/build/staden-io-lib-1.14.15'
make[3]: Entering directory '/build/staden-io-lib-1.14.15'
/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/bin'
/usr/bin/install -c io_lib-config '/build/staden-io-lib-1.14.15/debian/tmp/usr/bin'
/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/build/staden-io-lib-1.14.15/debian/tmp/usr/share/man/man1'
/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/share/man/man3'
/usr/bin/install -c -m 644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/build/staden-io-lib-1.14.15/debian/tmp/usr/share/man/man3'
/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/share/man/man4'
/usr/bin/install -c -m 644 man/man4/Read.4 '/build/staden-io-lib-1.14.15/debian/tmp/usr/share/man/man4'
/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/include/io_lib'
/usr/bin/install -c -m 644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/cram_bambam.h '/build/staden-io-lib-1.14.15/debian/tmp/usr/include/io_lib'
/usr/bin/install -c -m 644 io_lib/zfio.h io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h io_lib/version.h '/build/staden-io-lib-1.14.15/debian/tmp/usr/include/io_lib'
make[3]: Leaving directory '/build/staden-io-lib-1.14.15'
make[2]: Leaving directory '/build/staden-io-lib-1.14.15'
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
debian/rules override_dh_install-arch
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
dh_install -a
mkdir -p /build/staden-io-lib-1.14.15/debian/libstaden-read-dev/usr/bin
mv /build/staden-io-lib-1.14.15/debian/staden-io-lib-utils/usr/bin/io_lib-config /build/staden-io-lib-1.14.15/debian/libstaden-read-dev/usr/bin
#
# Call d-shlibmove to comply with library packaging guide
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--movedev "debian/tmp/usr/include" usr \
--override s/libhtscodecs2-dev/libhtscodecs-dev/ \
debian/tmp/usr/lib/*/libstaden-read.so
Library package automatic movement utility
--> libbz2-dev package exists.
--> libcurl4-gnutls-dev package exists.
--> libhtscodecs-dev package exists.
--> liblzma-dev package exists.
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libstaden-read-dev/usr/lib/i386-linux-gnu
install -d -m 755 debian/libstaden-read14/usr/lib/i386-linux-gnu
mv debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.a debian/libstaden-read-dev/usr/lib/i386-linux-gnu
mv debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.so debian/libstaden-read-dev/usr/lib/i386-linux-gnu
mv /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.so.14 debian/libstaden-read14/usr/lib/i386-linux-gnu
mv /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/i386-linux-gnu/libstaden-read.so.14.1.2 debian/libstaden-read14/usr/lib/i386-linux-gnu
PKGDEV=libstaden-read-dev
PKGSHL=libstaden-read14
install -d -m 755 debian/libstaden-read-dev/usr
mv debian/tmp/usr/include debian/libstaden-read-dev/usr
mkdir -p /build/staden-io-lib-1.14.15/debian/libstaden-read-dev/usr/include/io_lib/
cp /build/staden-io-lib-1.14.15/io_lib_config.h /build/staden-io-lib-1.14.15/debian/libstaden-read-dev/usr/include/io_lib/
# make sure io_lib-config --libs will not return -pie (see #825461)
find debian/*/usr/bin -name io_lib-config -exec sed -i -e 's/ *-fPIE//' -e 's/ *-pie//' \{\} \;
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
debian/rules override_dh_install-indep
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
dh_install -i
mkdir -p debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test
# fix path to staden-io-lib executable in examples
for tst in `ls tests/*.test` ; do \
sed -e 's#\.\./$top_builddir/progs/#/usr/bin/#' -e 's#$top_builddir/progs/#/usr/bin/#' ${tst} > debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/`basename ${tst}` ; \
done
# remove autogenerated big data files
rm -f debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/data/ce\#*sorted.sam
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
dh_installdocs -O--no-parallel
dh_installchangelogs -O--no-parallel
dh_installman -O--no-parallel
dh_installsystemduser -O--no-parallel
dh_lintian -O--no-parallel
dh_perl -O--no-parallel
dh_link -O--no-parallel
dh_strip_nondeterminism -O--no-parallel
dh_compress -O--no-parallel
debian/rules override_dh_fixperms-indep
make[1]: Entering directory '/build/staden-io-lib-1.14.15'
dh_fixperms
chmod +x debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.test debian/staden-io-lib-examples/usr/share/doc/staden-io-lib/test/*.pl
make[1]: Leaving directory '/build/staden-io-lib-1.14.15'
dh_fixperms -O--no-parallel -Nstaden-io-lib-examples
dh_missing -O--no-parallel -Nstaden-io-lib-examples
dh_dwz -a -O--no-parallel
dh_strip -a -O--no-parallel
dh_makeshlibs -a -O--no-parallel
dh_shlibdeps -a -O--no-parallel
dh_installdeb -O--no-parallel
dh_gencontrol -O--no-parallel
dh_md5sums -O--no-parallel
dh_builddeb -O--no-parallel
dpkg-deb: building package 'libstaden-read-dev' in '../libstaden-read-dev_1.14.15-1_i386.deb'.
dpkg-deb: building package 'staden-io-lib-utils-dbgsym' in '../staden-io-lib-utils-dbgsym_1.14.15-1_i386.deb'.
dpkg-deb: building package 'staden-io-lib-utils' in '../staden-io-lib-utils_1.14.15-1_i386.deb'.
dpkg-deb: building package 'libstaden-read14' in '../libstaden-read14_1.14.15-1_i386.deb'.
dpkg-deb: building package 'libstaden-read14-dbgsym' in '../libstaden-read14-dbgsym_1.14.15-1_i386.deb'.
dpkg-deb: building package 'staden-io-lib-examples' in '../staden-io-lib-examples_1.14.15-1_all.deb'.
dpkg-genbuildinfo --build=binary -O../staden-io-lib_1.14.15-1_i386.buildinfo
dpkg-genchanges --build=binary -O../staden-io-lib_1.14.15-1_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: 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/130031 and its subdirectories
I: Current time: Wed Jul 3 12:18:38 -12 2024
I: pbuilder-time-stamp: 1720052318
Thu Jun 1 17:55:39 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net.
Thu Jun 1 17:55:39 UTC 2023 I: Preparing to do remote build '2' on ionos2-i386.debian.net.
Thu Jun 1 18:14:44 UTC 2023 I: Deleting $TMPDIR on ionos2-i386.debian.net.
Thu Jun 1 18:14:44 UTC 2023 I: staden-io-lib_1.14.15-1_i386.changes:
Format: 1.8
Date: Tue, 14 Mar 2023 07:41:05 +0100
Source: staden-io-lib
Binary: libstaden-read-dev libstaden-read14 libstaden-read14-dbgsym staden-io-lib-examples staden-io-lib-utils staden-io-lib-utils-dbgsym
Architecture: i386 all
Version: 1.14.15-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libstaden-read-dev - development files for libstaden-read
libstaden-read14 - Staden library for reading and writing DNA sequencing results
staden-io-lib-examples - programs for manipulating DNA sequencing files (usage examples)
staden-io-lib-utils - programs for manipulating DNA sequencing files
Changes:
staden-io-lib (1.14.15-1) unstable; urgency=medium
.
* New upstream version (bugfix release needed for salmon)
* Patch applied in previous package was included upstream
Checksums-Sha1:
a4ff4509c0cd07c0be0eb3811e6448b335eba37f 370104 libstaden-read-dev_1.14.15-1_i386.deb
577ba76b0eeb0ff9f78a1e0960a6ea5e3efd3221 496704 libstaden-read14-dbgsym_1.14.15-1_i386.deb
aecee421bda1e964bfaf9e1fe97f9a2b44f14c98 286980 libstaden-read14_1.14.15-1_i386.deb
14bbaa74c4f7279c99306a6acaebb4d08483ae92 2753664 staden-io-lib-examples_1.14.15-1_all.deb
191b28c3d130ca017357014651b014b7d8f0adb4 342932 staden-io-lib-utils-dbgsym_1.14.15-1_i386.deb
18b3cc02c3ca9e3ad52d8cc04a62b1690830a85e 176092 staden-io-lib-utils_1.14.15-1_i386.deb
148f11b4c65020faabe30aeb096b4496ed83a6c4 7332 staden-io-lib_1.14.15-1_i386.buildinfo
Checksums-Sha256:
ee197a47a7565658d05c2de616f2ccd486e25a15c46cb63efa9705031f3d0f2a 370104 libstaden-read-dev_1.14.15-1_i386.deb
237f775fa7329f0f9ff20d88dfd2bb963d9c722af7928bcfff66af328a3ae09d 496704 libstaden-read14-dbgsym_1.14.15-1_i386.deb
3861c60583104c6e5448fa86aac59376654e18fb5daafb613adc8cb89e9e9a1d 286980 libstaden-read14_1.14.15-1_i386.deb
24051bfab2f197a26b46e1ef23002d3a0b4985a7db8a03ee9c9946539fdb0a23 2753664 staden-io-lib-examples_1.14.15-1_all.deb
ab85e634f897394ca5f593a63091df35d914c4d67fbe19e3ac4c051b5a697944 342932 staden-io-lib-utils-dbgsym_1.14.15-1_i386.deb
dc06eccc654e99f43ee9cef67c98db11fded18321c02deaacf21689a9125ab6f 176092 staden-io-lib-utils_1.14.15-1_i386.deb
70ffb5c75f4d48719e8ac80586ad7a2c4bf8d55a5762613fbe4c6eacd83724a8 7332 staden-io-lib_1.14.15-1_i386.buildinfo
Files:
b72e56fc62e63223b3db8b0c0fca1992 370104 libdevel optional libstaden-read-dev_1.14.15-1_i386.deb
ef7eae756ccde46efa099e0c8e4872d7 496704 debug optional libstaden-read14-dbgsym_1.14.15-1_i386.deb
8b3fe704a18d5e9825916468b8cf723c 286980 libs optional libstaden-read14_1.14.15-1_i386.deb
46ff58780401e658f52ec714d6193a06 2753664 science optional staden-io-lib-examples_1.14.15-1_all.deb
bc5b93cdb79ad2826294b352dcc221ba 342932 debug optional staden-io-lib-utils-dbgsym_1.14.15-1_i386.deb
565c77f5806e978ba030c17914a20a0b 176092 science optional staden-io-lib-utils_1.14.15-1_i386.deb
2227de53598b42fb09a0761d164e8f0d 7332 science optional staden-io-lib_1.14.15-1_i386.buildinfo
Thu Jun 1 18:14:45 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.HrCAmrxX/staden-io-lib_1.14.15-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.HrCAmrxX/staden-io-lib_1.14.15-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.HrCAmrxX/staden-io-lib_1.14.15-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.HrCAmrxX/b1/staden-io-lib_1.14.15-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.HrCAmrxX/b2/staden-io-lib_1.14.15-1_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.400s)
0.400s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.076s)
0.075s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.001s)
0.001s 1 call specialize
Thu Jun 1 18:14:46 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Thu Jun 1 18:14:46 UTC 2023 I: staden-io-lib from bookworm built successfully and reproducibly on i386.
Thu Jun 1 18:14:48 UTC 2023 I: Submitting .buildinfo files to external archives:
Thu Jun 1 18:14:48 UTC 2023 I: Submitting 12K b1/staden-io-lib_1.14.15-1_i386.buildinfo.asc
Thu Jun 1 18:14:49 UTC 2023 I: Submitting 12K b2/staden-io-lib_1.14.15-1_i386.buildinfo.asc
Thu Jun 1 18:14:49 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Jun 1 18:14:49 UTC 2023 I: Done submitting .buildinfo files.
Thu Jun 1 18:14:49 UTC 2023 I: Removing signed staden-io-lib_1.14.15-1_i386.buildinfo.asc files:
removed './b1/staden-io-lib_1.14.15-1_i386.buildinfo.asc'
removed './b2/staden-io-lib_1.14.15-1_i386.buildinfo.asc'