I: pbuilder: network access will be disabled during build
I: Current time: Fri Jun 21 23:50:24 +14 2024
I: pbuilder-time-stamp: 1718963424
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: 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 Tue Mar 14 21:04:22 2023 +14
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/1665988/tmp/hooks/D01_modify_environment starting
debug: Running on ionos5-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jun 21 23:50 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/1665988/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/1665988/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=f4f9a1fbec50496688a9e5383a9aeef5
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=1665988
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ah8bZva1/pbuilderrc_00th --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ah8bZva1/b2 --logfile b2/build.log --extrapackages usrmerge staden-io-lib_1.14.15-1.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://85.184.249.68:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 21 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 21 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 21 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 6 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 21 2022 date
-rwxr-xr-x 1 root root 89240 Sep 21 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 21 2022 df
-rwxr-xr-x 1 root root 151344 Sep 21 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 25 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 21 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 24 2023 login
-rwxr-xr-x 1 root root 151344 Sep 21 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 24 2023 more
-rwsr-xr-x 1 root root 59704 Mar 24 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 21 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 6 2023 sed
lrwxrwxrwx 1 root root 9 Jun 21 23:50 sh -> /bin/bash
-rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 21 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 24 2023 su
-rwxr-xr-x 1 root root 39824 Sep 21 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 7 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 21 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 21 2022 true
-rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 24 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/1665988/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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 ... 19596 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 24.7 MB of archives. After unpacking 84.3 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-9 [481 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs-dev amd64 1.3.0-4 [2866 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Fetched 24.7 MB in 0s (92.4 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19596 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_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_amd64.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 ...
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Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ...
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Setting up libbz2-dev:amd64 (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) ...
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Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
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Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
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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
Reading package lists...
Building dependency tree...
Reading state information...
usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/1665988/tmp/hooks/A99_set_merged_usr starting
Re-configuring usrmerge...
removed '/etc/unsupported-skip-usrmerge-conversion'
The system has been successfully converted.
I: user script /srv/workspace/pbuilder/1665988/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/staden-io-lib-1.14.15/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../staden-io-lib_1.14.15-1_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 amd64
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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/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... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for sys/param.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for gawk... (cached) mawk
checking for curl-config... /usr/bin/curl-config
checking for the version of libcurl... 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) /usr/bin/grep -E
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for fcntl.h... yes
checking for limits.h... yes
checking for unistd.h... (cached) yes
checking for malloc.h... yes
checking for zlib.h... (cached) yes
checking for stdio_ext.h... yes
checking whether byte ordering is bigendian... (cached) no
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking for inline... inline
checking for mode_t... yes
checking for fileno... yes
checking for fstat... yes
checking for mallopt... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -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/sh ../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/x86_64-linux-gnu libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -lcurl -lhtscodecs -lm -llzma -lbz2
libtool: link: gcc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lz -lcurl -lhtscodecs -lm -llzma -lbz2 -g -O2 -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/sh ../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/sh ../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/sh ../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/sh ../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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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/sh ../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'
/usr/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/lib/x86_64-linux-gnu'
/bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/staden-io-lib-1.14.15/debian/tmp/usr/lib/x86_64-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/x86_64-linux-gnu/libstaden-read.so.14.1.2
libtool: install: (cd /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu/libstaden-read.a
libtool: install: chmod 644 /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a
libtool: install: ranlib /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a
libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/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'
/usr/bin/mkdir -p '/build/staden-io-lib-1.14.15/debian/tmp/usr/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/build/staden-io-lib-1.14.15/debian/tmp/usr/bin'
libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/x86_64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/convert_trace /build/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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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'
/usr/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'
/usr/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'
/usr/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'
/usr/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'
/usr/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/x86_64-linux-gnu
install -d -m 755 debian/libstaden-read14/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.a debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so debian/libstaden-read-dev/usr/lib/x86_64-linux-gnu
mv /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14 debian/libstaden-read14/usr/lib/x86_64-linux-gnu
mv /build/staden-io-lib-1.14.15/debian/tmp/usr/lib/x86_64-linux-gnu/libstaden-read.so.14.1.2 debian/libstaden-read14/usr/lib/x86_64-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 'staden-io-lib-utils' in '../staden-io-lib-utils_1.14.15-1_amd64.deb'.
dpkg-deb: building package 'staden-io-lib-utils-dbgsym' in '../staden-io-lib-utils-dbgsym_1.14.15-1_amd64.deb'.
dpkg-deb: building package 'libstaden-read-dev' in '../libstaden-read-dev_1.14.15-1_amd64.deb'.
dpkg-deb: building package 'libstaden-read14' in '../libstaden-read14_1.14.15-1_amd64.deb'.
dpkg-deb: building package 'libstaden-read14-dbgsym' in '../libstaden-read14-dbgsym_1.14.15-1_amd64.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_amd64.buildinfo
dpkg-genchanges --build=binary -O../staden-io-lib_1.14.15-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/1665988/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/1665988/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/1665988 and its subdirectories
I: Current time: Fri Jun 21 23:57:02 +14 2024
I: pbuilder-time-stamp: 1718963822