I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 22 22:30:44 +14 2022 I: pbuilder-time-stamp: 1663835444 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_1.14.13-4.dsc] I: copying [./staden-io-lib_1.14.13.orig.tar.gz] I: copying [./staden-io-lib_1.14.13-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.aq2qk4Et/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 29 00:42:51 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./staden-io-lib_1.14.13-4.dsc dpkg-source: info: extracting staden-io-lib in staden-io-lib-1.14.13 dpkg-source: info: unpacking staden-io-lib_1.14.13.orig.tar.gz dpkg-source: info: unpacking staden-io-lib_1.14.13-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 32-bit.patch dpkg-source: info: applying pathmax.patch dpkg-source: info: applying fix_fseeko.patch dpkg-source: info: applying spelling dpkg-source: info: applying usedebianhtscodecs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31654/tmp/hooks/D01_modify_environment starting debug: Running on codethink9-arm64. 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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/31654/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/31654/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=31654 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/tmp.Ab7IcthsIB/pbuilderrc_RSiL --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Ab7IcthsIB/b2 --logfile b2/build.log staden-io-lib_1.14.13-4.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 5 2021 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Jul 29 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 29 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Jul 29 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 29 2021 more -rwsr-xr-x 1 root root 51360 Jul 29 2021 mount -rwxr-xr-x 1 root root 14496 Jul 29 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Sep 22 22:30 sh -> bash lrwxrwxrwx 1 root root 4 Sep 19 05:48 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Jul 29 2021 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 29 2021 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 29 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/31654/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libcurl4-gnutls-dev | libcurl4-nss-dev, libhtscodecs-dev, d-shlibs dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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. 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} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhtscodecs-dev{a} libhtscodecs2{a} libicu67{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{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: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 22.4 MB of archives. After unpacking 76.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 d-shlibs all 0.98 [17.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+b1 [419 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libhtscodecs2 arm64 0.5-3 [48.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libhtscodecs-dev arm64 0.5-3 [2518 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Fetched 22.4 MB in 1s (38.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../10-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../16-d-shlibs_0.98_all.deb ... Unpacking d-shlibs (0.98) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../24-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../26-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. 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Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/staden-io-lib-1.14.13/ && 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_1.14.13-4_source.changes dpkg-buildpackage: info: source package staden-io-lib dpkg-buildpackage: info: source version 1.14.13-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan 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]: Map '/build/staden-io-lib-1.14.13' wordt verlaten 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: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]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan export ac_cv_func_mmap_fixed_mapped=yes && dh_auto_configure ./configure --build=aarch64-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/aarch64-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 thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for grep that handles long lines and -e... (cached) /bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 7.74.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... 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... no checking for lzma_easy_buffer_encode in -llzma... no checking for bsc_compress in -lbsc... no checking whether byte ordering is bigendian... no checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for zlib.h... (cached) yes checking stdio_ext.h usability... yes checking stdio_ext.h presence... 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 stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... (cached) yes checking for library containing pthread_join... -lpthread 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-1.14.13/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 make[1]: Map '/build/staden-io-lib-1.14.13' wordt verlaten dh_auto_build -O--no-parallel make -j1 make[1]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan make all-recursive make[2]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan Making all in io_lib make[3]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt binnengegaan /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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o 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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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c 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compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat 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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c 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--tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o In file included from /usr/include/string.h:495, from bam.c:44: In function ‘memcpy’, inlined from ‘bam_cigar2tag’ at bam.c:1794:5, inlined from ‘bam_put_seq’ at bam.c:3891:10: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:34:10: warning: writing 8 bytes into a region of size 1 [-Wstringop-overflow=] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bam.c:59: bam.c: In function ‘bam_put_seq’: ../io_lib/bam.h:102:19: note: at offset 0 to object ‘data’ with size 1 declared here 102 | unsigned char data; /* unknown size */ | ^~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 15:0:1 -Wl,-z,relro -Wl,-z,now -o libstaden-read.la -rpath /usr/lib/aarch64-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 -lpthread 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 -lpthread -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.14.1.0 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.14" && ln -s "libstaden-read.so.14.1.0" "libstaden-read.so.14") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.14.1.0" "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]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt verlaten Making all in progs make[3]: Map '/build/staden-io-lib-1.14.13/progs' wordt binnengegaan gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 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-I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extract_qual.o extract_qual.c /bin/sh ../libtool --tag=CC --mode=link gcc 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../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_info.o srf_info.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o srf_list.o srf_list.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_exp.o hash_exp.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scramble.o scramble.c /bin/sh ../libtool --tag=CC --mode=link gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o scramble scramble.o ../io_lib/libstaden-read.la -lm -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread make[3]: Map '/build/staden-io-lib-1.14.13/progs' wordt verlaten Making all in tests make[3]: Map '/build/staden-io-lib-1.14.13/tests' wordt binnengegaan gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../htscodecs -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread libtool: link: gcc -Wall -g -O2 -fdebug-prefix-map=/build/staden-io-lib-1.14.13=. -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 -lpthread make[3]: Map '/build/staden-io-lib-1.14.13/tests' wordt verlaten make[3]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan make[3]: Map '/build/staden-io-lib-1.14.13' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13' wordt verlaten make[1]: Map '/build/staden-io-lib-1.14.13' wordt verlaten debian/rules override_dh_auto_test-indep make[1]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan echo "Do not run test suite for architecture independent builds" Do not run test suite for architecture independent builds make[1]: Map '/build/staden-io-lib-1.14.13' wordt verlaten dh_auto_test -O--no-parallel -Nstaden-io-lib-examples make -j1 check VERBOSE=1 make[1]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan Making check in io_lib make[2]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt binnengegaan make[2]: Er hoeft niets gedaan te worden voor 'check'. make[2]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt verlaten Making check in progs make[2]: Map '/build/staden-io-lib-1.14.13/progs' wordt binnengegaan make[2]: Er hoeft niets gedaan te worden voor 'check'. make[2]: Map '/build/staden-io-lib-1.14.13/progs' wordt verlaten Making check in tests make[2]: Map '/build/staden-io-lib-1.14.13/tests' wordt binnengegaan make check-TESTS make[3]: Map '/build/staden-io-lib-1.14.13/tests' wordt binnengegaan 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 ../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 ../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 ../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 ../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 ../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 ../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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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. ../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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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. ../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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -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 is not a 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 -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 is not a 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 -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 is not a recognised GA4GH standard. Note this 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -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 is not a 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 -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 is not a 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -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 is not a 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 -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 is not a 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -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 is not a 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 -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 is not a 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -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 is not a 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 -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 is not a 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. 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 -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 is not a recognised GA4GH standard. Note this 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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 -V3.1 -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 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. ../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. ../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. ../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 Cannot open file test.out/aux#aux.full.cram 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]: Map '/build/staden-io-lib-1.14.13/tests' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13/tests' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan make[2]: Map '/build/staden-io-lib-1.14.13' wordt verlaten make[1]: Map '/build/staden-io-lib-1.14.13' wordt verlaten 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-1.14.13/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan Making install in io_lib make[2]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt binnengegaan make[3]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt binnengegaan /bin/mkdir -p '/build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.14.1.0 /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.so.14.1.0 libtool: install: (cd /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libstaden-read.so.14.1.0 libstaden-read.so.14 || { rm -f libstaden-read.so.14 && ln -s libstaden-read.so.14.1.0 libstaden-read.so.14; }; }) libtool: install: (cd /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libstaden-read.so.14.1.0 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.14.1.0 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.a libtool: install: chmod 644 /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.a libtool: install: ranlib /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' make[3]: Er hoeft niets gedaan te worden voor 'install-data-am'. make[3]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13/io_lib' wordt verlaten Making install in progs make[2]: Map '/build/staden-io-lib-1.14.13/progs' wordt binnengegaan make[3]: Map '/build/staden-io-lib-1.14.13/progs' wordt binnengegaan /bin/mkdir -p '/build/staden-io-lib-1.14.13/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-1.14.13/debian/tmp/usr/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/convert_trace /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/makeSCF /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_seq /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_qual /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/extract_fastq /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_dump /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_info /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scf_update /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/get_comment /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_tar /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_extract /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_list /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/trace_dump /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_sff /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/append_sff /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/ztr_dump /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_dump_all /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_index_hash /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_linear /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_extract_hash /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fastq /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf2fasta /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_filter /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_info /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/srf_list /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/hash_exp /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_dump /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_index /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scramble /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_merge /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_pileup /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_flagstat /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/scram_test /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_size /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/cram_filter /build/staden-io-lib-1.14.13/debian/tmp/usr/bin/cram_filter make[3]: Er hoeft niets gedaan te worden voor 'install-data-am'. make[3]: Map '/build/staden-io-lib-1.14.13/progs' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13/progs' wordt verlaten Making install in tests make[2]: Map '/build/staden-io-lib-1.14.13/tests' wordt binnengegaan make[3]: Map '/build/staden-io-lib-1.14.13/tests' wordt binnengegaan make[3]: Er hoeft niets gedaan te worden voor 'install-exec-am'. make[3]: Er hoeft niets gedaan te worden voor 'install-data-am'. make[3]: Map '/build/staden-io-lib-1.14.13/tests' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13/tests' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan make[3]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan /bin/mkdir -p '/build/staden-io-lib-1.14.13/debian/tmp/usr/bin' /usr/bin/install -c io_lib-config '/build/staden-io-lib-1.14.13/debian/tmp/usr/bin' /bin/mkdir -p '/build/staden-io-lib-1.14.13/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-1.14.13/debian/tmp/usr/share/man/man1' /bin/mkdir -p '/build/staden-io-lib-1.14.13/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-1.14.13/debian/tmp/usr/share/man/man3' /bin/mkdir -p '/build/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man4' /usr/bin/install -c -m 644 man/man4/Read.4 '/build/staden-io-lib-1.14.13/debian/tmp/usr/share/man/man4' /bin/mkdir -p '/build/staden-io-lib-1.14.13/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-1.14.13/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-1.14.13/debian/tmp/usr/include/io_lib' make[3]: Map '/build/staden-io-lib-1.14.13' wordt verlaten make[2]: Map '/build/staden-io-lib-1.14.13' wordt verlaten make[1]: Map '/build/staden-io-lib-1.14.13' wordt verlaten debian/rules override_dh_install-arch make[1]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan dh_install -a mkdir -p /build/staden-io-lib-1.14.13/debian/libstaden-read-dev/usr/bin mv /build/staden-io-lib-1.14.13/debian/staden-io-lib-utils/usr/bin/io_lib-config /build/staden-io-lib-1.14.13/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 --> libcurl4-gnutls-dev package exists. --> libhtscodecs-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libstaden-read-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libstaden-read14/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.a debian/libstaden-read-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.so debian/libstaden-read-dev/usr/lib/aarch64-linux-gnu mv /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.so.14 debian/libstaden-read14/usr/lib/aarch64-linux-gnu mv /build/staden-io-lib-1.14.13/debian/tmp/usr/lib/aarch64-linux-gnu/libstaden-read.so.14.1.0 debian/libstaden-read14/usr/lib/aarch64-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-1.14.13/debian/libstaden-read-dev/usr/include/io_lib/ cp /build/staden-io-lib-1.14.13/io_lib_config.h /build/staden-io-lib-1.14.13/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]: Map '/build/staden-io-lib-1.14.13' wordt verlaten debian/rules override_dh_install-indep make[1]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan 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]: Map '/build/staden-io-lib-1.14.13' wordt verlaten 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]: Map '/build/staden-io-lib-1.14.13' wordt binnengegaan 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]: Map '/build/staden-io-lib-1.14.13' wordt verlaten 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: pakket 'libstaden-read14' wordt gebouwd in '../libstaden-read14_1.14.13-4_arm64.deb'. dpkg-deb: pakket 'staden-io-lib-utils-dbgsym' wordt gebouwd in '../staden-io-lib-utils-dbgsym_1.14.13-4_arm64.deb'. dpkg-deb: pakket 'libstaden-read-dev' wordt gebouwd in '../libstaden-read-dev_1.14.13-4_arm64.deb'. dpkg-deb: pakket 'libstaden-read14-dbgsym' wordt gebouwd in '../libstaden-read14-dbgsym_1.14.13-4_arm64.deb'. dpkg-deb: pakket 'staden-io-lib-utils' wordt gebouwd in '../staden-io-lib-utils_1.14.13-4_arm64.deb'. dpkg-deb: pakket 'staden-io-lib-examples' wordt gebouwd in '../staden-io-lib-examples_1.14.13-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../staden-io-lib_1.14.13-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/31654/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/31654/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/31654 and its subdirectories I: Current time: Thu Sep 22 22:45:57 +14 2022 I: pbuilder-time-stamp: 1663836357