I: pbuilder: network access will be disabled during build
I: Current time: Sat Nov 23 07:45:45 +14 2024
I: pbuilder-time-stamp: 1732297545
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [samtools_1.21-0+exp1.dsc]
I: copying [./samtools_1.21.orig.tar.gz]
I: copying [./samtools_1.21-0+exp1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Nov 14 19:30:19 2024 
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./samtools_1.21-0+exp1.dsc: no acceptable signature found
dpkg-source: info: extracting samtools in samtools-1.21
dpkg-source: info: unpacking samtools_1.21.orig.tar.gz
dpkg-source: info: unpacking samtools_1.21-0+exp1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying reproducible.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D01_modify_environment starting
debug: Running on virt64a.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Nov 22 17:45 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/20800/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
  BASH_VERSION='5.2.32(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=armhf
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
  DIRSTACK=()
  DISTRIBUTION=experimental
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=arm
  HOST_ARCH=armhf
  IFS=' 	
  '
  INVOCATION_ID=9b34ed21d43f4555ac03c1401bbfe047
  LANG=C
  LANGUAGE=it_CH:it
  LC_ALL=C
  MACHTYPE=arm-unknown-linux-gnueabihf
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnueabihf
  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=20800
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/pbuilderrc_RhZo --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RfmZQeJi/b2 --logfile b2/build.log samtools_1.21-0+exp1.dsc'
  SUDO_GID=114
  SUDO_UID=108
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://10.0.0.15:3142/
I: uname -a
  Linux i-capture-the-hostname 6.1.0-27-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Aug  4 21:30 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/20800/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: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.21~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19686 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 bash-completion; however:
  Package bash-completion is not installed.
 pbuilder-satisfydepends-dummy depends on libio-pty-perl; however:
  Package libio-pty-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libncurses-dev; however:
  Package libncurses-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.21~); however:
  Package libhts-dev is not installed.
 pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
  Package zlib1g-dev is not installed.
 pbuilder-satisfydepends-dummy depends on automake; however:
  Package automake is not installed.
 pbuilder-satisfydepends-dummy depends on autoconf-archive; however:
  Package autoconf-archive is not installed.
 pbuilder-satisfydepends-dummy depends on pkgconf; however:
  Package pkgconf is not installed.
 pbuilder-satisfydepends-dummy depends on tabix; however:
  Package tabix is not installed.
 pbuilder-satisfydepends-dummy depends on liblzma-dev; however:
  Package liblzma-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
  Package libbz2-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{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} libbz2-dev{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libpipeline1{a} libpkgconf3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  bzip2-doc curl libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl lynx wget 
0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.5 MB of archives. After unpacking 84.3 MB will be used.
The following packages have unmet dependencies:
 pbuilder-satisfydepends-dummy : Depends: libhts-dev (>= 1.21~) but it is not going to be installed
The following actions will resolve these dependencies:

      Install the following packages:                                 
1)      comerr-dev [2.1-1.47.1-1+b1 (unstable)]                       
2)      krb5-multidev [1.21.3-3 (unstable)]                           
3)      libbrotli-dev [1.1.0-2+b6 (unstable)]                         
4)      libbrotli1 [1.1.0-2+b6 (unstable)]                            
5)      libcom-err2 [1.47.1-1+b1 (unstable)]                          
6)      libcurl3t64-gnutls [8.11.0-1 (unstable)]                      
7)      libcurl4-gnutls-dev [8.11.0-1 (unstable)]                     
8)      libdeflate-dev [1.22-1 (unstable)]                            
9)      libevent-2.1-7t64 [2.1.12-stable-10+b1 (unstable)]            
10)     libgmp-dev [2:6.3.0+dfsg-2+b2 (unstable)]                     
11)     libgmpxx4ldbl [2:6.3.0+dfsg-2+b2 (unstable)]                  
12)     libgnutls-dane0t64 [3.8.8-2 (unstable)]                       
13)     libgnutls-openssl27t64 [3.8.8-2 (unstable)]                   
14)     libgnutls28-dev [3.8.8-2 (unstable)]                          
15)     libgssapi-krb5-2 [1.21.3-3 (unstable)]                        
16)     libgssrpc4t64 [1.21.3-3 (unstable)]                           
17)     libhts-dev [1.21+ds-0+exp2 (experimental)]                    
18)     libhts3t64 [1.21+ds-0+exp2 (experimental)]                    
19)     libidn2-dev [2.3.7-2+b1 (unstable)]                           
20)     libk5crypto3 [1.21.3-3 (unstable)]                            
21)     libkadm5clnt-mit12 [1.21.3-3 (unstable)]                      
22)     libkadm5srv-mit12 [1.21.3-3 (unstable)]                       
23)     libkdb5-10t64 [1.21.3-3 (unstable)]                           
24)     libkeyutils1 [1.6.3-4 (unstable)]                             
25)     libkrb5-3 [1.21.3-3 (unstable)]                               
26)     libkrb5-dev [1.21.3-3 (unstable)]                             
27)     libkrb5support0 [1.21.3-3 (unstable)]                         
28)     libldap-2.5-0 [2.5.18+dfsg-3+b1 (unstable)]                   
29)     libldap-dev [2.6.8+dfsg-1~exp4+b1 (experimental)]             
30)     libldap2 [2.6.8+dfsg-1~exp4+b1 (experimental)]                
31)     libnghttp2-14 [1.64.0-1 (unstable)]                           
32)     libnghttp2-dev [1.64.0-1 (unstable)]                          
33)     libnghttp3-9 [1.4.0-1+b1 (unstable)]                          
34)     libnghttp3-dev [1.4.0-1+b1 (unstable)]                        
35)     libngtcp2-16 [1.6.0-1 (unstable)]                             
36)     libngtcp2-crypto-gnutls-dev [1.6.0-1 (unstable)]              
37)     libngtcp2-crypto-gnutls8 [1.6.0-1 (unstable)]                 
38)     libngtcp2-dev [1.6.0-1 (unstable)]                            
39)     libp11-kit-dev [0.25.5-2+b1 (unstable)]                       
40)     libpsl-dev [0.21.2-1.1+b1 (unstable)]                         
41)     libpsl5t64 [0.21.2-1.1+b1 (unstable)]                         
42)     librtmp-dev [2.4+20151223.gitfa8646d.1-2+b5 (unstable)]       
43)     librtmp1 [2.4+20151223.gitfa8646d.1-2+b5 (unstable)]          
44)     libsasl2-2 [2.1.28+dfsg1-8 (unstable)]                        
45)     libsasl2-modules-db [2.1.28+dfsg1-8 (unstable)]               
46)     libssh2-1-dev [1.11.1-1 (unstable)]                           
47)     libssh2-1t64 [1.11.1-1 (unstable)]                            
48)     libssl-dev [3.4.0-1 (experimental)]                           
49)     libtasn1-6-dev [4.19.0-3+b3 (unstable)]                       
50)     libunbound8 [1.22.0-1 (unstable)]                             
51)     libzstd-dev [1.5.6+dfsg-1+b1 (unstable)]                      
52)     nettle-dev [3.10-1+b1 (unstable)]                             

      Upgrade the following packages:                                 
53)     libssl3t64 [3.3.2-2 (now, unstable) -> 3.4.0-1 (experimental)]



The following NEW packages will be installed:
  autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} 
The following packages will be upgraded:
  libssl3t64 
The following packages are RECOMMENDED but will NOT be installed:
  bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 
1 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded.
Need to get 39.1 MB of archives. After unpacking 126 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main armhf autoconf-archive all 20220903-3 [775 kB]
Get: 2 http://deb.debian.org/debian experimental/main armhf libssl3t64 armhf 3.4.0-1 [1883 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf bash-completion all 1:2.14.0-2 [310 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.1-1+b1 [54.3 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 22 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 27 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 31 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB]
Get: 32 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 33 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 34 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB]
Get: 35 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB]
Get: 36 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB]
Get: 37 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B]
Get: 38 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB]
Get: 39 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB]
Get: 40 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-3 [52.5 kB]
Get: 41 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [37.0 kB]
Get: 42 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-3 [37.1 kB]
Get: 43 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [46.7 kB]
Get: 44 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-3 [126 kB]
Get: 45 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB]
Get: 46 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB]
Get: 47 http://deb.debian.org/debian unstable/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB]
Get: 48 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB]
Get: 49 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB]
Get: 50 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB]
Get: 51 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB]
Get: 52 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.4.0-1+b1 [55.0 kB]
Get: 53 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB]
Get: 54 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB]
Get: 55 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB]
Get: 56 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB]
Get: 57 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB]
Get: 58 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.11.0-1 [310 kB]
Get: 59 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB]
Get: 60 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1 [539 kB]
Get: 61 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB]
Get: 62 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB]
Get: 63 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB]
Get: 64 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-2+b1 [208 kB]
Get: 65 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB]
Get: 66 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB]
Get: 67 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB]
Get: 68 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB]
Get: 69 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB]
Get: 70 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-3 [15.8 kB]
Get: 71 http://deb.debian.org/debian experimental/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4+b1 [162 kB]
Get: 72 http://deb.debian.org/debian experimental/main armhf libldap-dev armhf 2.6.8+dfsg-1~exp4+b1 [282 kB]
Get: 73 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB]
Get: 74 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB]
Get: 75 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB]
Get: 76 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB]
Get: 77 http://deb.debian.org/debian unstable/main armhf libnghttp3-dev armhf 1.4.0-1+b1 [79.8 kB]
Get: 78 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls-dev armhf 1.6.0-1 [22.1 kB]
Get: 79 http://deb.debian.org/debian unstable/main armhf libngtcp2-dev armhf 1.6.0-1 [168 kB]
Get: 80 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB]
Get: 81 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB]
Get: 82 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB]
Get: 83 http://deb.debian.org/debian experimental/main armhf libssl-dev armhf 3.4.0-1 [2428 kB]
Get: 84 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB]
Get: 85 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-1+b1 [327 kB]
Get: 86 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.11.0-1 [434 kB]
Get: 87 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB]
Get: 88 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.22-1 [44.5 kB]
Get: 89 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB]
Get: 90 http://deb.debian.org/debian experimental/main armhf libhts3t64 armhf 1.21+ds-0+exp2 [407 kB]
Get: 91 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.3-1+b1 [304 kB]
Get: 92 http://deb.debian.org/debian experimental/main armhf libhts-dev armhf 1.21+ds-0+exp2 [1655 kB]
Get: 93 http://deb.debian.org/debian unstable/main armhf libio-pty-perl armhf 1:1.20-1+b2 [33.8 kB]
Get: 94 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2+b1 [82.3 kB]
Get: 95 http://deb.debian.org/debian unstable/main armhf libncurses-dev armhf 6.5-2+b1 [310 kB]
Get: 96 http://deb.debian.org/debian unstable/main armhf tabix armhf 1.20+ds-2 [418 kB]
Fetched 39.1 MB in 1s (26.4 MB/s)
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Unpacking libzstd-dev:armhf (1.5.6+dfsg-1+b1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../83-libcurl4-gnutls-dev_8.11.0-1_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (8.11.0-1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../84-libdeflate0_1.22-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.22-1) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../85-libdeflate-dev_1.22-1_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.22-1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../86-libhtscodecs2_1.6.1-1_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.6.1-1) ...
Selecting previously unselected package libhts3t64:armhf.
Preparing to unpack .../87-libhts3t64_1.21+ds-0+exp2_armhf.deb ...
Unpacking libhts3t64:armhf (1.21+ds-0+exp2) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../88-liblzma-dev_5.6.3-1+b1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.6.3-1+b1) ...
Selecting previously unselected package libhts-dev:armhf.
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Unpacking libhts-dev:armhf (1.21+ds-0+exp2) ...
Selecting previously unselected package libio-pty-perl.
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Unpacking libio-pty-perl (1:1.20-1+b2) ...
Selecting previously unselected package libncurses6:armhf.
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Unpacking libncurses6:armhf (6.5-2+b1) ...
Selecting previously unselected package libncurses-dev:armhf.
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Unpacking libncurses-dev:armhf (6.5-2+b1) ...
Selecting previously unselected package tabix.
Preparing to unpack .../93-tabix_1.20+ds-2_armhf.deb ...
Unpacking tabix (1.20+ds-2) ...
Setting up libhtscodecs2:armhf (1.6.1-1) ...
Setting up libpipeline1:armhf (1.5.8-1) ...
Setting up libgnutls-openssl27t64:armhf (3.8.8-2) ...
Setting up libkeyutils1:armhf (1.6.3-4) ...
Setting up libicu72:armhf (72.1-5+b1) ...
Setting up libzstd-dev:armhf (1.5.6+dfsg-1+b1) ...
Setting up bsdextrautils (2.40.2-11) ...
Setting up libio-pty-perl (1:1.20-1+b2) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libbrotli1:armhf (1.1.0-2+b6) ...
Setting up libmagic1t64:armhf (1:5.45-3+b1) ...
Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ...
Setting up libnghttp2-14:armhf (1.64.0-1) ...
Setting up libdeflate0:armhf (1.22-1) ...
Setting up gettext-base (0.22.5-2) ...
Setting up m4 (1.4.19-4) ...
Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ...
Setting up autoconf-archive (20220903-3) ...
Setting up libcom-err2:armhf (1.47.1-1+b1) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:armhf (0.192-4) ...
Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ...
Setting up libkrb5support0:armhf (1.21.3-3) ...
Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunbound8:armhf (1.22.0-1) ...
Setting up libpkgconf3:armhf (1.8.1-4) ...
Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-2+b2) ...
Setting up libgnutls-dane0t64:armhf (3.8.8-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up bash-completion (1:2.14.0-2) ...
Setting up libncurses6:armhf (6.5-2+b1) ...
Setting up comerr-dev:armhf (2.1-1.47.1-1+b1) ...
Setting up libssl-dev:armhf (3.4.0-1) ...
Setting up autopoint (0.22.5-2) ...
Setting up pkgconf-bin (1.8.1-4) ...
Setting up libk5crypto3:armhf (1.21.3-3) ...
Setting up libidn2-dev:armhf (2.3.7-2+b1) ...
Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ...
Setting up autoconf (2.72-3) ...
Setting up libnghttp3-9:armhf (1.4.0-1+b1) ...
Setting up libnghttp3-dev:armhf (1.4.0-1+b1) ...
Setting up liblzma-dev:armhf (5.6.3-1+b1) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:armhf (0.0.8-1+b2) ...
Setting up libngtcp2-16:armhf (1.6.0-1) ...
Setting up libkrb5-3:armhf (1.21.3-3) ...
Setting up libssh2-1t64:armhf (1.11.1-1) ...
Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ...
Setting up libdeflate-dev:armhf (1.22-1) ...
Setting up tabix (1.20+ds-2) ...
Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up libldap2:armhf (2.6.8+dfsg-1~exp4+b1) ...
Setting up libbrotli-dev:armhf (1.1.0-2+b6) ...
Setting up libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ...
Setting up libp11-kit-dev:armhf (0.25.5-2+b1) ...
Setting up libbz2-dev:armhf (1.0.8-6) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libncurses-dev:armhf (6.5-2+b1) ...
Setting up gettext (0.22.5-2) ...
Setting up libgmp-dev:armhf (2:6.3.0+dfsg-2+b2) ...
Setting up nettle-dev:armhf (3.10-1+b1) ...
Setting up libtool (2.4.7-8) ...
Setting up libngtcp2-crypto-gnutls-dev:armhf (1.6.0-1) ...
Setting up libngtcp2-dev:armhf (1.6.0-1) ...
Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ...
Setting up pkgconf:armhf (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libldap-dev:armhf (2.6.8+dfsg-1~exp4+b1) ...
Setting up libgssapi-krb5-2:armhf (1.21.3-3) ...
Setting up libssh2-1-dev:armhf (1.11.1-1) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-5) ...
Setting up libgnutls28-dev:armhf (3.8.8-2) ...
Setting up libnghttp2-dev:armhf (1.64.0-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libcurl3t64-gnutls:armhf (8.11.0-1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libgssrpc4t64:armhf (1.21.3-3) ...
Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libhts3t64:armhf (1.21+ds-0+exp2) ...
Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ...
Setting up libkdb5-10t64:armhf (1.21.3-3) ...
Setting up debhelper (13.20) ...
Setting up libkadm5srv-mit12:armhf (1.21.3-3) ...
Setting up krb5-multidev:armhf (1.21.3-3) ...
Setting up libkrb5-dev:armhf (1.21.3-3) ...
Setting up libcurl4-gnutls-dev:armhf (8.11.0-1) ...
Setting up libhts-dev:armhf (1.21+ds-0+exp2) ...
Processing triggers for libc-bin (2.40-3) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/20800/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for experimental
I: user script /srv/workspace/pbuilder/20800/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/samtools-1.21/ && 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  > ../samtools_1.21-0+exp1_source.changes
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.21-0+exp1
dpkg-buildpackage: info: source distribution experimental
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.21/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
rm -f config.mk
touch config.mk
dh_auto_clean --
	make -j4 distclean
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.fa.fai anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam*
cd test/reference && rm -f mpileup.*.fai
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
rm -rf autom4te.cache
make[2]: Leaving directory '/build/reproducible-path/samtools-1.21'
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files
	rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.before
	grep -q ^XDT_ configure.ac
	autoreconf -f -i
configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.after
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
touch config.mk
aclocal --force -I debian/ -I /usr/share/aclocal
autoconf
configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:64: the top level
dh_auto_configure -- --with-htslib=system
	./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
checking for gawk... no
checking for mawk... mawk
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for gcc option to enable large file support... none needed
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for Curses library... yes
checking for working curses.h... yes
checking for X/Open Enhanced Curses conformance... no
checking for Curses color functions... yes
checking for obsolete Curses functions... yes
checking for library containing cbreak... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
	rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
dh_auto_build -- \
  CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
  CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
  LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
	make -j4 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now"
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
echo '#define SAMTOOLS_VERSION "1.21"' > version.h
echo '#define SAMTOOLS_CC "gcc"' >> version.h
echo '#define SAMTOOLS_CPPFLAGS "-frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h
echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security"' >> version.h
echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h
echo '#define SAMTOOLS_HTSDIR ""' >> version.h
echo '#define SAMTOOLS_LIBS ""' >> version.h
echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h
sed -i -e 's@/build/reproducible-path/samtools-1.21@�BUILDPATH�@g' version.h
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DMAQ_LONGREADS -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I.  -I./lz4 -frelease  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
cc1: warning: command-line option '-frelease' is valid for D but not for C
ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz 
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz 
gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz 
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz  -lpthread
gcc  -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz  -lpthread
make[2]: Leaving directory '/build/reproducible-path/samtools-1.21'
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
	rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
dh_auto_test -- BGZIP=/usr/bin/bgzip
	make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-}
test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram
.. ok

test_reference:
	/build/reproducible-path/samtools-1.21/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram
.. ok

/usr/bin/bgzip -c -b 65272 -s 5 /tmp/lLvf1KLWi4/bgzip.dat.gz
.. ok

/usr/bin/bgzip -c -b 979200 -s 6 /tmp/lLvf1KLWi4/bgzip.dat.gz
.. ok

/usr/bin/bgzip -c -b 652804 -s 6 /tmp/lLvf1KLWi4/bgzip.dat.gz
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 3:11-13 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 2:998-1003 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 1:100-104 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools faidx /tmp/lLvf1KLWi4/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 3:11-13
.. ok

.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 3:11-13
.. ok

.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 2:998-1003
.. ok

.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 2:998-1003
.. ok

.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 1:100-104
.. ok

.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 1:100-104
.. ok

.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq 1:99998-100007
.. ok

.. ok

/build/reproducible-path/samtools-1.21/samtools fqidx /tmp/lLvf1KLWi4/fqidx.fq.gz 1:99998-100007
.. ok

.. ok

test_dict:
	/build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/reproducible-path/samtools-1.21/test/dat/dict.fa
.. ok

test_dict:
	/build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/lLvf1KLWi4/dict.fa.gz
.. ok

test_dict:
	cat /build/reproducible-path/samtools-1.21/test/dat/dict.fa | /build/reproducible-path/samtools-1.21/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz
.. ok

test_dict:
	/build/reproducible-path/samtools-1.21/samtools dict -AH < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa
.. ok

test_dict:
	/build/reproducible-path/samtools-1.21/samtools dict -H -l /build/reproducible-path/samtools-1.21/test/dat/dict.alt < /build/reproducible-path/samtools-1.21/test/dat/dict.alias.fa
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view /tmp/lLvf1KLWi4/large_chrom.bam ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view /tmp/lLvf1KLWi4/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools merge -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/lLvf1KLWi4/test_input_1_b.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/lLvf1KLWi4/auto_indexed.crai && cat /tmp/lLvf1KLWi4/auto_indexed.crai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/lLvf1KLWi4/large_chrom.bam ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -@ 2 /tmp/lLvf1KLWi4/large_chrom.bam ref2:1-541556283
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai /tmp/lLvf1KLWi4/test_input_1_b.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /tmp/lLvf1KLWi4/test_input_1_b_opt.bam.bai ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -@ 2 -M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam && cat /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam.bai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools view -@ 2 -X /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam.bai ref2
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -@ 2 /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.cram /tmp/lLvf1KLWi4/auto_indexed.crai && cat /tmp/lLvf1KLWi4/auto_indexed.crai
.. ok

test_index:
	/build/reproducible-path/samtools-1.21/samtools index -@ 2 -c /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.sam /tmp/lLvf1KLWi4/auto_indexed.csi && cat /tmp/lLvf1KLWi4/auto_indexed.csi
.. ok

test_mpileup:
	/build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.bam.list -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.cram.list -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.bam.urllist -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/build/reproducible-path/samtools-1.21/samtools mpileup -b /tmp/lLvf1KLWi4/mpileup.cram.urllist -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:100-150
.. ok

test_mpileup:
	/build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lLvf1KLWi4/mpileup.1.bam | grep -v mpileup
.. ok

test_mpileup:
	/build/reproducible-path/samtools-1.21/samtools mpileup -B --ff 0x14 -f /tmp/lLvf1KLWi4/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lLvf1KLWi4/mpileup.1.cram | grep -v mpileup
.. ok

test_mpileup:
	/build/reproducible-path/samtools-1.21/samtools mpileup /build/reproducible-path/samtools-1.21/test/mpileup/overlap.bam | grep 128814202
.. ok

test_usage:
	samtools
	samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version
.. ok

test_usage_subcommand:
	samtools dict

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools faidx
.. ok

test_usage_subcommand:
	samtools fqidx
.. ok

test_usage_subcommand:
	samtools index
.. ok

test_usage_subcommand:
	samtools calmd

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools fixmate
.. ok

test_usage_subcommand:
	samtools reheader

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools targetcut

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools addreplacerg
.. ok

test_usage_subcommand:
	samtools markdup

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools ampliconclip

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools collate
.. ok

test_usage_subcommand:
	samtools cat

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools consensus
.. ok

test_usage_subcommand:
	samtools merge
.. ok

test_usage_subcommand:
	samtools mpileup

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools sort
.. ok

test_usage_subcommand:
	samtools split
.. ok

test_usage_subcommand:
	samtools quickcheck
.. ok

test_usage_subcommand:
	samtools fastq
.. ok

test_usage_subcommand:
	samtools fasta
.. ok

test_usage_subcommand:
	samtools import
.. ok

test_usage_subcommand:
	samtools reference
.. ok

test_usage_subcommand:
	samtools reset
.. ok

test_usage_subcommand:
	samtools bedcov

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools coverage
.. ok

test_usage_subcommand:
	samtools depth
.. ok

test_usage_subcommand:
	samtools flagstat
.. ok

test_usage_subcommand:
	samtools idxstats
.. ok

test_usage_subcommand:
	samtools phase

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools stats
.. ok

test_usage_subcommand:
	samtools ampliconstats
.. ok

test_usage_subcommand:
	samtools flags
.. ok

test_usage_subcommand:
	samtools head
.. ok

test_usage_subcommand:
	samtools tview

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools view
.. ok

test_usage_subcommand:
	samtools depad

	Usage on stderr rather than stdout
.. expected failure

test_usage_subcommand:
	samtools samples

	Usage on stderr rather than stdout
.. expected failure

test_view:
	Generating test data file .................. done
	1: SAM -> BAM -> SAM                                        .. ok

	2: SAM -> uncompressed BAM                                  .. ok

	3: uncompressed BAM -> SAM and compare                      .. ok

	4: SAM -> fast compressed BAM                               .. ok

	5: fast compressed BAM -> SAM and compare                   .. ok

	6: SAM -> CRAM -> SAM (UR header tags)                      .. ok

	7: SAM -> CRAM -> SAM (M5 header tags)                      .. ok

	8: BAM -> CRAM with UR -> SAM                               .. ok

	9: SAM -> BAM (M5 header tags)                              .. ok

	10: SAM -> BAM -> CRAM -> SAM (M5 header tags)              .. ok

	11: CRAM -> BAM with UR                                     .. ok

	12: CRAM -> BAM with M5                                     .. ok

	13: SAM -> SAM via stdout                                   .. ok

	14: SAM -> BAM via stdout                                   .. ok

	15: SAM -> CRAM via stdout                                  .. ok

	16: SAM from stdin -> SAM                                   .. ok

	17: BAM from stdin -> SAM                                   .. ok

	18: CRAM from stdin -> SAM                                  .. ok

	19: samtools view -H (SAM input)                            .. ok

	20: samtools view -H (BAM input)                            .. ok

	21: samtools view -H (CRAM input)                           .. ok

	22: No headers (SAM input)                                  .. ok

	23: No headers (BAM input)                                  .. ok

	24: No headers (CRAM input)                                 .. ok

	25: Filter -f 128 (SAM input)                               .. ok

	26: Count -f 128 (SAM input)                                .. ok

	27: Filter -f 128 (BAM input)                               .. ok

	28: Count -f 128 (BAM input)                                .. ok

	29: Filter -f 128 (CRAM input)                              .. ok

	30: Count -f 128 (CRAM input)                               .. ok

	31: Filter -F 128 (SAM input)                               .. ok

	32: Count -F 128 (SAM input)                                .. ok

	33: Filter -F 128 (BAM input)                               .. ok

	34: Count -F 128 (BAM input)                                .. ok

	35: Filter -F 128 (CRAM input)                              .. ok

	36: Count -F 128 (CRAM input)                               .. ok

	37: Filter -F 128 -f 2 (SAM input)                          .. ok

	38: Count -F 128 -f 2 (SAM input)                           .. ok

	39: Filter -F 128 -f 2 (BAM input)                          .. ok

	40: Count -F 128 -f 2 (BAM input)                           .. ok

	41: Filter -F 128 -f 2 (CRAM input)                         .. ok

	42: Count -F 128 -f 2 (CRAM input)                          .. ok

	43: Filter -r grp2 (SAM input)                              .. ok

	44: Count -r grp2 (SAM input)                               .. ok

	45: Filter -r grp2 (BAM input)                              .. ok

	46: Count -r grp2 (BAM input)                               .. ok

	47: Filter -r grp2 (CRAM input)                             .. ok

	48: Count -r grp2 (CRAM input)                              .. ok

	49: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input)     .. ok

	50: Count -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input)      .. ok

	51: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input)     .. ok

	52: Count -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input)      .. ok

	53: Filter -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input)    .. ok

	54: Count -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input)     .. ok

	55: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (SAM input).. ok

	56: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (SAM input).. ok

	57: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (BAM input).. ok

	58: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (BAM input).. ok

	59: Filter -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (CRAM input).. ok

	60: Count -R /tmp/lLvf1KLWi4/view.001.fogn -r grp2 (CRAM input).. ok

	61: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input).. ok

	62: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (SAM input).. ok

	63: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input).. ok

	64: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (BAM input).. ok

	65: Filter -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok

	66: Count -r grp2 -R /tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok

	67: Filter -N /tmp/lLvf1KLWi4/view.001.forn (SAM input)     .. ok

	68: Count -N /tmp/lLvf1KLWi4/view.001.forn (SAM input)      .. ok

	69: Filter -N /tmp/lLvf1KLWi4/view.001.forn (BAM input)     .. ok

	70: Count -N /tmp/lLvf1KLWi4/view.001.forn (BAM input)      .. ok

	71: Filter -N /tmp/lLvf1KLWi4/view.001.forn (CRAM input)    .. ok

	72: Count -N /tmp/lLvf1KLWi4/view.001.forn (CRAM input)     .. ok

	73: Filter -d BC (SAM input)                                .. ok

	74: Count -d BC (SAM input)                                 .. ok

	75: Filter -d BC (BAM input)                                .. ok

	76: Count -d BC (BAM input)                                 .. ok

	77: Filter -d BC (CRAM input)                               .. ok

	78: Count -d BC (CRAM input)                                .. ok

	79: Filter -d BC:TGCA (SAM input)                           .. ok

	80: Count -d BC:TGCA (SAM input)                            .. ok

	81: Filter -d BC:TGCA (BAM input)                           .. ok

	82: Count -d BC:TGCA (BAM input)                            .. ok

	83: Filter -d BC:TGCA (CRAM input)                          .. ok

	84: Count -d BC:TGCA (CRAM input)                           .. ok

	85: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)  .. ok

	86: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)   .. ok

	87: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)  .. ok

	88: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)   .. ok

	89: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input) .. ok

	90: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input)  .. ok

	91: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (SAM input).. ok

	92: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (SAM input).. ok

	93: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (BAM input).. ok

	94: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (BAM input).. ok

	95: Filter -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (CRAM input).. ok

	96: Count -D BC:/tmp/lLvf1KLWi4/view.001.fobc -d BC:TGCA (CRAM input).. ok

	97: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input).. ok

	98: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (SAM input).. ok

	99: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input).. ok

	100: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (BAM input).. ok

	101: Filter -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input).. ok

	102: Count -d BC:TGCA -D BC:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input).. ok

	103: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (SAM input) .. ok

	104: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (SAM input)  .. ok

	105: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (BAM input) .. ok

	106: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (BAM input)  .. ok

	107: Filter -D RG:/tmp/lLvf1KLWi4/view.001.fogn (CRAM input).. ok

	108: Count -D RG:/tmp/lLvf1KLWi4/view.001.fogn (CRAM input) .. ok

	109: Filter -d NE:TGCA (SAM input)                          .. ok

	110: Count -d NE:TGCA (SAM input)                           .. ok

	111: Filter -d NE:TGCA (BAM input)                          .. ok

	112: Count -d NE:TGCA (BAM input)                           .. ok

	113: Filter -d NE:TGCA (CRAM input)                         .. ok

	114: Count -d NE:TGCA (CRAM input)                          .. ok

	115: Filter -d TGCA (SAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test115.sam -h -d TGCA /tmp/lLvf1KLWi4/view.001.sam --no-PG


.. expected failure

	116: Count -d TGCA (SAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/view.001.sam --no-PG


.. expected failure

	117: Filter -d TGCA (BAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test117.sam -h -d TGCA /tmp/lLvf1KLWi4/view.test001.bam --no-PG


.. expected failure

	118: Count -d TGCA (BAM input)                              samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/view.test001.bam --no-PG


.. expected failure

	119: Filter -d TGCA (CRAM input)                            samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test119.sam -h -d TGCA /tmp/lLvf1KLWi4/view.test006.cram --no-PG


.. expected failure

	120: Count -d TGCA (CRAM input)                             samtools view: Invalid "tag:value" option: "TGCA"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -d TGCA /tmp/lLvf1KLWi4/view.test006.cram --no-PG


.. expected failure

	121: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test121.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.001.sam --no-PG


.. expected failure

	122: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.001.sam --no-PG


.. expected failure

	123: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test123.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test001.bam --no-PG


.. expected failure

	124: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test001.bam --no-PG


.. expected failure

	125: Filter -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test125.sam -h -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test006.cram --no-PG


.. expected failure

	126: Count -D BClong:/tmp/lLvf1KLWi4/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/lLvf1KLWi4/view.001.fobc"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -D BClong:/tmp/lLvf1KLWi4/view.001.fobc /tmp/lLvf1KLWi4/view.test006.cram --no-PG


.. expected failure

	127: Filter -d BC:ACGT -d RG:grp2 (SAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/view.001.sam --no-PG


.. expected failure

	128: Count -d BC:ACGT -d RG:grp2 (SAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/view.001.sam --no-PG


.. expected failure

	129: Filter -d BC:ACGT -d RG:grp2 (BAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/view.test001.bam --no-PG


.. expected failure

	130: Count -d BC:ACGT -d RG:grp2 (BAM input)                samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/view.test001.bam --no-PG


.. expected failure

	131: Filter -d BC:ACGT -d RG:grp2 (CRAM input)              samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -o /tmp/lLvf1KLWi4/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/view.test006.cram --no-PG


.. expected failure

	132: Count -d BC:ACGT -d RG:grp2 (CRAM input)               samtools view: Different tag "BC" was specified before: "RG:grp2"
	Failed command:
	/build/reproducible-path/samtools-1.21/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/lLvf1KLWi4/view.test006.cram --no-PG


.. expected failure

	133: Filter -d NM:13 (SAM input)                            .. ok

	134: Count -d NM:13 (SAM input)                             .. ok

	135: Filter -d NM:13 (BAM input)                            .. ok

	136: Count -d NM:13 (BAM input)                             .. ok

	137: Filter -d NM:13 (CRAM input)                           .. ok

	138: Count -d NM:13 (CRAM input)                            .. ok

	139: Filter -d ab:z (SAM input)                             .. ok

	140: Count -d ab:z (SAM input)                              .. ok

	141: Filter -d ab:z (BAM input)                             .. ok

	142: Count -d ab:z (BAM input)                              .. ok

	143: Filter -d ab:z (CRAM input)                            .. ok

	144: Count -d ab:z (CRAM input)                             .. ok

	145: Filter -l Library 2 (SAM input)                        .. ok

	146: Count -l Library 2 (SAM input)                         .. ok

	147: Filter -l Library 2 (BAM input)                        .. ok

	148: Count -l Library 2 (BAM input)                         .. ok

	149: Filter -l Library 2 (CRAM input)                       .. ok

	150: Count -l Library 2 (CRAM input)                        .. ok

	151: Filter -l Library 3 (SAM input)                        .. ok

	152: Count -l Library 3 (SAM input)                         .. ok

	153: Filter -l Library 3 (BAM input)                        .. ok

	154: Count -l Library 3 (BAM input)                         .. ok

	155: Filter -l Library 3 (CRAM input)                       .. ok

	156: Count -l Library 3 (CRAM input)                        .. ok

	157: Filter -q 50 (SAM input)                               .. ok

	158: Count -q 50 (SAM input)                                .. ok

	159: Filter -q 50 (BAM input)                               .. ok

	160: Count -q 50 (BAM input)                                .. ok

	161: Filter -q 50 (CRAM input)                              .. ok

	162: Count -q 50 (CRAM input)                               .. ok

	163: Filter -q 99 (SAM input)                               .. ok

	164: Count -q 99 (SAM input)                                .. ok

	165: Filter -q 99 (BAM input)                               .. ok

	166: Count -q 99 (BAM input)                                .. ok

	167: Filter -q 99 (CRAM input)                              .. ok

	168: Count -q 99 (CRAM input)                               .. ok

	169: Filter -q 100 (SAM input)                              .. ok

	170: Count -q 100 (SAM input)                               .. ok

	171: Filter -q 100 (BAM input)                              .. ok

	172: Count -q 100 (BAM input)                               .. ok

	173: Filter -q 100 (CRAM input)                             .. ok

	174: Count -q 100 (CRAM input)                              .. ok

	175: Filter -x fa (SAM input)                               .. ok

	176: Count -x fa (SAM input)                                .. ok

	177: Filter -x fa (BAM input)                               .. ok

	178: Count -x fa (BAM input)                                .. ok

	179: Filter -x fa (CRAM input)                              .. ok

	180: Count -x fa (CRAM input)                               .. ok

	181: Filter -x fa -x ha (SAM input)                         .. ok

	182: Count -x fa -x ha (SAM input)                          .. ok

	183: Filter -x fa -x ha (BAM input)                         .. ok

	184: Count -x fa -x ha (BAM input)                          .. ok

	185: Filter -x fa -x ha (CRAM input)                        .. ok

	186: Count -x fa -x ha (CRAM input)                         .. ok

	187: Filter -x fa,ha (SAM input)                            .. ok

	188: Count -x fa,ha (SAM input)                             .. ok

	189: Filter -x fa,ha (BAM input)                            .. ok

	190: Count -x fa,ha (BAM input)                             .. ok

	191: Filter -x fa,ha (CRAM input)                           .. ok

	192: Count -x fa,ha (CRAM input)                            .. ok

	193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok

	201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok

	203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok

	205: Filter -x fa -r grp2 (SAM input)                       .. ok

	206: Count -x fa -r grp2 (SAM input)                        .. ok

	207: Filter -x fa -r grp2 (BAM input)                       .. ok

	208: Count -x fa -r grp2 (BAM input)                        .. ok

	209: Filter -x fa -r grp2 (CRAM input)                      .. ok

	210: Count -x fa -r grp2 (CRAM input)                       .. ok

	211: Filter -x RG -r grp2 (SAM input)                       .. ok

	212: Count -x RG -r grp2 (SAM input)                        .. ok

	213: Filter -x RG -r grp2 (BAM input)                       .. ok

	214: Count -x RG -r grp2 (BAM input)                        .. ok

	215: Filter -x RG -r grp2 (CRAM input)                      .. ok

	216: Count -x RG -r grp2 (CRAM input)                       .. ok

	217: Filter -m 10 (SAM input)                               .. ok

	218: Count -m 10 (SAM input)                                .. ok

	219: Filter -m 10 (BAM input)                               .. ok

	220: Count -m 10 (BAM input)                                .. ok

	221: Filter -m 10 (CRAM input)                              .. ok

	222: Count -m 10 (CRAM input)                               .. ok

	223: Filter -m 11 (SAM input)                               .. ok

	224: Count -m 11 (SAM input)                                .. ok

	225: Filter -m 11 (BAM input)                               .. ok

	226: Count -m 11 (BAM input)                                .. ok

	227: Filter -m 11 (CRAM input)                              .. ok

	228: Count -m 11 (CRAM input)                               .. ok

	229: Filter -m 15 (SAM input)                               .. ok

	230: Count -m 15 (SAM input)                                .. ok

	231: Filter -m 15 (BAM input)                               .. ok

	232: Count -m 15 (BAM input)                                .. ok

	233: Filter -m 15 (CRAM input)                              .. ok

	234: Count -m 15 (CRAM input)                               .. ok

	235: Filter -m 16 (SAM input)                               .. ok

	236: Count -m 16 (SAM input)                                .. ok

	237: Filter -m 16 (BAM input)                               .. ok

	238: Count -m 16 (BAM input)                                .. ok

	239: Filter -m 16 (CRAM input)                              .. ok

	240: Count -m 16 (CRAM input)                               .. ok

	241: Filter -e !(flag & 128) && (flag & 2) (SAM input)      .. ok

	242: Count -e !(flag & 128) && (flag & 2) (SAM input)       .. ok

	243: Filter -e !(flag & 128) && (flag & 2) (BAM input)      .. ok

	244: Count -e !(flag & 128) && (flag & 2) (BAM input)       .. ok

	245: Filter -e !(flag & 128) && (flag & 2) (CRAM input)     .. ok

	246: Count -e !(flag & 128) && (flag & 2) (CRAM input)      .. ok

	247: Filter -e [BC] (SAM input)                             .. ok

	248: Count -e [BC] (SAM input)                              .. ok

	249: Filter -e [BC] (BAM input)                             .. ok

	250: Count -e [BC] (BAM input)                              .. ok

	251: Filter -e [BC] (CRAM input)                            .. ok

	252: Count -e [BC] (CRAM input)                             .. ok

	253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok

	255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok

	257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok

	259: Filter -e mapq >= 50 (SAM input)                       .. ok

	260: Count -e mapq >= 50 (SAM input)                        .. ok

	261: Filter -e mapq >= 50 (BAM input)                       .. ok

	262: Count -e mapq >= 50 (BAM input)                        .. ok

	263: Filter -e mapq >= 50 (CRAM input)                      .. ok

	264: Count -e mapq >= 50 (CRAM input)                       .. ok

	265: Filter -e mapq >= 99 (SAM input)                       .. ok

	266: Count -e mapq >= 99 (SAM input)                        .. ok

	267: Filter -e mapq >= 99 (BAM input)                       .. ok

	268: Count -e mapq >= 99 (BAM input)                        .. ok

	269: Filter -e mapq >= 99 (CRAM input)                      .. ok

	270: Count -e mapq >= 99 (CRAM input)                       .. ok

	271: Filter -e mapq >= 100 (SAM input)                      .. ok

	272: Count -e mapq >= 100 (SAM input)                       .. ok

	273: Filter -e mapq >= 100 (BAM input)                      .. ok

	274: Count -e mapq >= 100 (BAM input)                       .. ok

	275: Filter -e mapq >= 100 (CRAM input)                     .. ok

	276: Count -e mapq >= 100 (CRAM input)                      .. ok

	277: 1bp reads file SAM -> BAM -> SAM                       .. ok

	278: 1bp reads file SAM -> CRAM -> SAM                      .. ok

	278: Region  Z (BAM input)                                  .. ok

	279: Count  Z (BAM input)                                   .. ok

	280: Region  Z (CRAM input)                                 .. ok

	281: Count  Z (CRAM input)                                  .. ok

	282: Region  Z:30 (BAM input)                               .. ok

	283: Count  Z:30 (BAM input)                                .. ok

	284: Region  Z:30 (CRAM input)                              .. ok

	285: Count  Z:30 (CRAM input)                               .. ok

	286: Region  Z:20-40 (BAM input)                            .. ok

	287: Count  Z:20-40 (BAM input)                             .. ok

	288: Region  Z:20-40 (CRAM input)                           .. ok

	289: Count  Z:20-40 (CRAM input)                            .. ok

	290: Region  ref1 (BAM input)                               .. ok

	291: Count  ref1 (BAM input)                                .. ok

	292: Region  ref1 (CRAM input)                              .. ok

	293: Count  ref1 (CRAM input)                               .. ok

	294: Region  ref1:15 (BAM input)                            .. ok

	295: Count  ref1:15 (BAM input)                             .. ok

	296: Region  ref1:15 (CRAM input)                           .. ok

	297: Count  ref1:15 (CRAM input)                            .. ok

	298: Region  ref1:15-45 (BAM input)                         .. ok

	299: Count  ref1:15-45 (BAM input)                          .. ok

	300: Region  ref1:15-45 (CRAM input)                        .. ok

	301: Count  ref1:15-45 (CRAM input)                         .. ok

	302: Region  ref1:15-45 ref2 (BAM input)                    .. ok

	303: Count  ref1:15-45 ref2 (BAM input)                     .. ok

	304: Region  ref1:15-45 ref2 (CRAM input)                   .. ok

	305: Count  ref1:15-45 ref2 (CRAM input)                    .. ok

	306: Region  ref1:15-45 ref2:16 (BAM input)                 .. ok

	307: Count  ref1:15-45 ref2:16 (BAM input)                  .. ok

	308: Region  ref1:15-45 ref2:16 (CRAM input)                .. ok

	309: Count  ref1:15-45 ref2:16 (CRAM input)                 .. ok

	310: Region  ref1:15-45 ref2:16-31 (BAM input)              .. ok

	311: Count  ref1:15-45 ref2:16-31 (BAM input)               .. ok

	312: Region  ref1:15-45 ref2:16-31 (CRAM input)             .. ok

	313: Count  ref1:15-45 ref2:16-31 (CRAM input)              .. ok

	314: Region  ref1:15-15 ref1:45-45 (BAM input)              .. ok

	315: Count  ref1:15-15 ref1:45-45 (BAM input)               .. ok

	316: Region  ref1:15-15 ref1:45-45 (CRAM input)             .. ok

	317: Count  ref1:15-15 ref1:45-45 (CRAM input)              .. ok

	318: Region -f 128 ref1 (BAM input)                         .. ok

	319: Count -f 128 ref1 (BAM input)                          .. ok

	320: Region -f 128 ref1 (CRAM input)                        .. ok

	321: Count -f 128 ref1 (CRAM input)                         .. ok

	322: Region -q 50 ref1:15-45 (BAM input)                    .. ok

	323: Count -q 50 ref1:15-45 (BAM input)                     .. ok

	324: Region -q 50 ref1:15-45 (CRAM input)                   .. ok

	325: Count -q 50 ref1:15-45 (CRAM input)                    .. ok

	326: Region -r grp2 ref1:15-45 (BAM input)                  .. ok

	327: Count -r grp2 ref1:15-45 (BAM input)                   .. ok

	328: Region -r grp2 ref1:15-45 (CRAM input)                 .. ok

	329: Count -r grp2 ref1:15-45 (CRAM input)                  .. ok

	330: Region  * (BAM input)                                  .. ok

	331: Count  * (BAM input)                                   .. ok

	332: Region  * (CRAM input)                                 .. ok

	333: Count  * (CRAM input)                                  .. ok

	334: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed  (BAM input).. ok

	335: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed  (BAM input).. ok

	336: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed  (CRAM input).. ok

	337: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed  (CRAM input).. ok

	338: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed  (BAM input).. ok

	339: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed  (BAM input).. ok

	340: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed  (CRAM input).. ok

	341: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.02.bed  (CRAM input).. ok

	342: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed  (BAM input).. ok

	343: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed  (BAM input).. ok

	344: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed  (CRAM input).. ok

	345: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed  (CRAM input).. ok

	346: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed  (BAM input).. ok

	347: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed  (BAM input).. ok

	348: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed  (CRAM input).. ok

	349: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.02.bed  (CRAM input).. ok

	350: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed  (BAM input).. ok

	351: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed  (BAM input).. ok

	352: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed  (CRAM input).. ok

	353: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.03.bed  (CRAM input).. ok

	354: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok

	355: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (BAM input).. ok

	356: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok

	357: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z (CRAM input).. ok

	358: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	359: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (BAM input).. ok

	360: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	361: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:30 (CRAM input).. ok

	362: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	363: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok

	364: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	365: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok

	366: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	367: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok

	368: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	369: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok

	370: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	371: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok

	372: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	373: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok

	374: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok

	375: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (BAM input).. ok

	376: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	377: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref2 (CRAM input).. ok

	378: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	379: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok

	380: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	381: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok

	382: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	383: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1  (BAM input).. ok

	384: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	385: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1  (CRAM input).. ok

	386: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	387: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128  (BAM input).. ok

	388: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	389: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -f 128  (CRAM input).. ok

	390: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	391: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5  (BAM input).. ok

	392: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	393: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -q 5  (CRAM input).. ok

	394: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	395: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok

	396: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	397: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok

	398: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	399: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap  (BAM input).. ok

	400: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	401: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap  (CRAM input).. ok

	402: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	403: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok

	404: Region -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	405: Count -L /build/reproducible-path/samtools-1.21/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok

	406: -L with nested regions                                 .. ok

	407: Make BAM with no M5/UR tags                            .. ok

	408: Add @SQ with -t (SAM -> SAM)                           .. ok

	409: Add @SQ with -T (SAM -> SAM)                           .. ok

	410: Add @SQ with -t (BAM -> SAM)                           .. ok

	411: Add @SQ with -T (BAM -> SAM)                           .. ok

	412: Add @SQ with -t (SAM -> BAM)                           .. ok

	413: Add @SQ with -T (SAM -> BAM)                           .. ok

	414: Add @SQ with -t (BAM -> BAM)                           .. ok

	415: Add @SQ with -T (BAM -> BAM)                           .. ok

	416: Add @SQ with -t (SAM -> CRAM)                          .. ok

	417: Add @SQ with -T (SAM -> CRAM)                          .. ok

	418: Add @SQ with -t (BAM -> CRAM)                          .. ok

	419: Add @SQ with -T (BAM -> CRAM)                          .. ok

	420: Make CRAM with no UR field                             .. ok

	421: Decoding CRAM with no UR field via -T                  .. ok

	422: CIGAR B-operator removal                               .. ok

	423: Big SAM -> BAM                                         .. ok

	424: Big SAM -> BAM (2 threads)                             .. ok

	425: Big SAM -> BAM (4 threads)                             .. ok

	426: Big SAM -> CRAM                                        .. ok

	427: Big SAM -> CRAM (2 threads)                            .. ok

	428: Big SAM -> CRAM (4 threads)                            .. ok

	429: Subsample 0.2 (SAM input) ............ ok

	430: Subsample 0.5 (SAM input) ............ ok

	431: Subsample 0.8 (SAM input) ............ ok

	432: Subsample 0.2 (BAM input) ............ ok

	433: Subsample 0.5 (BAM input) ............ ok

	434: Subsample 0.8 (BAM input) ............ ok

	435: Subsample 0.2 (CRAM input) ............ ok

	436: Subsample 0.5 (CRAM input) ............ ok

	437: Subsample 0.8 (CRAM input) ............ ok

	438: SAM add PG                                             .. ok

	439: Unset dup flag, remove dt and do tags                  .. ok

	440: Unmap dup flagged reads.                               .. ok

	441: Unmap dup flagged reads.                               .. ok

	442: fetch pairs                                            .. ok

	443: fetch pairs                                            .. ok

	444: fetch pairs                                            .. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -h 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -h 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -h 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -h 29 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -h 30 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -n 0 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -n 1 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -n 5 /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_head:
	/build/reproducible-path/samtools-1.21/samtools head -h 5 -n 5 < /build/reproducible-path/samtools-1.21/test/dat/view.001.sam
.. ok

test_cat:
	Generating test data file .................. done
	Generate BAM file #1                                        .. ok

	Generate BAM region file #1                                 .. ok

	Generate CRAM file #1                                       .. ok

	Generating test data file .................. done
	Generate BAM file #2                                        .. ok

	Generate BAM region file #2                                 .. ok

	Generate CRAM file #2                                       .. ok

	Generating test data file .................. done
	Generate BAM file #3                                        .. ok

	Generate BAM region file #3                                 .. ok

	Generate CRAM file #3                                       .. ok

	Generating test data file .................. done
	Generate BAM file #4                                        .. ok

	Generate BAM region file #4                                 .. ok

	Generate CRAM file #4                                       .. ok

	1: cat BAM files                                            .. ok

	2: cat recompressed BAM files                               .. ok

	3: cat CRAM files                                           .. ok

	4: cat CRAM subregion files                                 .. ok

	5: cat BAM files to stdout                                  .. ok

	6: cat recompressed BAM files to stdout                     .. ok

	7: cat CRAM files to stdout                                 .. ok

	8: cat CRAM subregion files to stdout                       .. ok

	9: cat CRAM part 1/2                                        .. ok

	9: cat CRAM part 2/2                                        .. ok

	9: cat CRAM parts 1/2 + 2/2                                 .. ok

	10: cat BAM files with new header                           .. ok

	11: cat recompressed BAM files with new header              .. ok

	12: cat CRAM files with new header                          .. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected  | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/1.1.fq.expected  | /build/reproducible-path/samtools-1.21/samtools fastq -0 /build/reproducible-path/samtools-1.21/test/0.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG -s test/bam2fq/5.s.fq.expected  | /build/reproducible-path/samtools-1.21/samtools fastq -s /build/reproducible-path/samtools-1.21/test/s.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/reproducible-path/samtools-1.21/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG	ID:rgid'
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/2.interleaved.fq -T ""
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/3.interleaved.fq -i
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T "*"
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T ""
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq
.. ok

test_import:
	/build/reproducible-path/samtools-1.21/samtools import --no-PG --i1 test/import/5-i1.fq --i2  test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ
.. ok

test_bam2fq:
	Generate BAM file                                           .. ok

	Generate CRAM file                                          .. ok

	1: fastq  (SAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input)                                       [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input)                                     [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input)                                      [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input)                                    [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fasta  -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -s /tmp/lLvf1KLWi4/bam2fq.discard.s.fq -0 /tmp/lLvf1KLWi4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq  -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	Generate BAM file (2 threads)                               .. ok

	Generate CRAM file (2 threads)                              .. ok

	1: fastq  (SAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	2: fastq -n (SAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	3: fastq  (BAM input) (2 threads)                           [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	4: fastq -n (BAM input) (2 threads)                         [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	5: fastq  (CRAM input) (2 threads)                          [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

	6: fastq -n (CRAM input) (2 threads)                        [M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 36 reads
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.002.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.003.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/bc.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.010.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/reproducible-path/samtools-1.21/test/bc_split.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T MD,ia -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.004.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/reproducible-path/samtools-1.21/test/i.fq -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/reproducible-path/samtools-1.21/test/s.fq -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.005.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -1 /build/reproducible-path/samtools-1.21/test/1.fq -2 /build/reproducible-path/samtools-1.21/test/2.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.703.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fq -2 /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fasta -@ 2 -N -1 /build/reproducible-path/samtools-1.21/test/o.fa -2 /build/reproducible-path/samtools-1.21/test/o.fa /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -o /build/reproducible-path/samtools-1.21/test/o.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -s /tmp/lLvf1KLWi4/bam2fq.discard.s.fq -0 /tmp/lLvf1KLWi4/bam2fq.discard.0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/reproducible-path/samtools-1.21/test/dat/bam2fq.013.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/reproducible-path/samtools-1.21/test/i1.fq --i2 /build/reproducible-path/samtools-1.21/test/i2.fq -0 /build/reproducible-path/samtools-1.21/test/0.fq /build/reproducible-path/samtools-1.21/test/dat/bam2fq.014.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -t -T '*' /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -N -T '*' -d ia /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_bam2fq:
	/build/reproducible-path/samtools-1.21/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/reproducible-path/samtools-1.21/test/dat/bam2fq.001.sam
.. ok

test_depad:
	Generate BAM file                                           .. ok

	depad  (SAM input)                                          .. ok

	depad -s (SAM input)                                        .. ok

	depad -u (SAM input)                                        .. ok

	depad -1 (SAM input)                                        .. ok

	depad  (BAM input)                                          .. ok

	depad -s (BAM input)                                        .. ok

	depad -u (BAM input)                                        .. ok

	depad -1 (BAM input)                                        .. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar_large.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa -i 0 /build/reproducible-path/samtools-1.21/test/stat/5_insert_cigar.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/7_supp.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/7_supp_large.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/8_secondary.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/8_secondary_large.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/1_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -S RG -r /build/reproducible-path/samtools-1.21/test/stat/test.fa /build/reproducible-path/samtools-1.21/test/stat/10_map_cigar.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -g 4 -t /build/reproducible-path/samtools-1.21/test/stat/11.stats.targets /build/reproducible-path/samtools-1.21/test/stat/11_target.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -g 4 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_3reads.bed | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/12_overlaps.bam -p -t /build/reproducible-path/samtools-1.21/test/stat/12_2reads.bed | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4

	/build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4

	/build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats /build/reproducible-path/samtools-1.21/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4

	/build/reproducible-path/samtools-1.21/test/stat/13.barcodes.fail.expected: No such file or directory
.. expected failure

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -I s1 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -I grp2 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -I grp3 /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -I Sample /build/reproducible-path/samtools-1.21/test/stat/11_target.bam | tail -n+4
.. ok

test_stats:
	/build/reproducible-path/samtools-1.21/samtools stats -r /build/reproducible-path/samtools-1.21/test/mpileup/ce.fa /build/reproducible-path/samtools-1.21/test/stat/15.big_del.sam | tail -n+4
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam -b /tmp/DwsJpoalnw - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.1.bam /tmp/lLvf1KLWi4/merge.tag.2.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.3.bam /tmp/lLvf1KLWi4/merge.tag.4.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/lLvf1KLWi4/merge.bed.1.bam /tmp/lLvf1KLWi4/merge.bed.2.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam -b /tmp/_oeRhjRfcI - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -r -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -cp -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -O sam - /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a_regex.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b_regex.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -o - -s 1 -O sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_c.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.1.bam /tmp/lLvf1KLWi4/merge.tag.2.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/lLvf1KLWi4/merge.tag.3.bam /tmp/lLvf1KLWi4/merge.tag.4.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM -L /build/reproducible-path/samtools-1.21/test/merge/merge.bed - /tmp/lLvf1KLWi4/merge.bed.1.bam /tmp/lLvf1KLWi4/merge.bed.2.bam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -r -O SAM - /build/reproducible-path/samtools-1.21/test/merge/test_no_pg_rg_co.sam
.. ok

test_merge:
	/build/reproducible-path/samtools-1.21/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.1.sam /build/reproducible-path/samtools-1.21/test/merge/test_template_coordinate.2.sam
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout.bam
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sorttmp
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -f /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sortout.bam
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -o /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam /tmp/lLvf1KLWi4/sorttmp
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -N -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_b.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -m 10M /build/reproducible-path/samtools-1.21/test/dat/sort_name_input_1.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -n -t RG -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t AS -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 -t FI -m 10M /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools sort -@ 2 --template-coordinate -m 10M /build/reproducible-path/samtools-1.21/test/sort/template-coordinate.sort.sam -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -M -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_sort:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/dat/auto_indexed.tmp.bam | /build/reproducible-path/samtools-1.21/samtools sort -@ 2 -MH -K10 -I /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa -O SAM -o -
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam  /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam  /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -O /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate1.tmp.sam  /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -@ 2 -o /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp.sam  /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate2.tmp
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_d.sam /build/reproducible-path/samtools-1.21/test/collate/collate3.tmp
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/1_fast_collate.sam
.. ok

test_collate:
	/build/reproducible-path/samtools-1.21/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/reproducible-path/samtools-1.21/test/collate/fast_collate.sam -o /build/reproducible-path/samtools-1.21/test/collate/2_fast_collate_with_tmp.sam
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/1_coord_sort.sam -

	ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.

.. expected failure

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/2_isize_overflow.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/5_ct.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -cO sam /build/reproducible-path/samtools-1.21/test/fixmate/6_ct_replace.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/7_two_read_mapped.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/8_isize_overflow_64bit.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -O sam /build/reproducible-path/samtools-1.21/test/fixmate/sanitize.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok+.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ok-.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_draft.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noML.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_not_updated_noMN.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bad_MN.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_MN_only.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_only.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_ML_wrong_len.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_noseq.sam -
.. ok

test_fixmate:
	/build/reproducible-path/samtools-1.21/samtools fixmate -@ 2 -M -z off -O sam /build/reproducible-path/samtools-1.21/test/fixmate/mod_bounds.sam -
.. ok

/build/reproducible-path/samtools-1.21/samtools calmd -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa
.. ok

/build/reproducible-path/samtools-1.21/samtools calmd -@ 2 -uAr /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam /build/reproducible-path/samtools-1.21/test/dat/mpileup.ref.fa
.. ok

test_idxstat:
	/build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
.. ok

test_idxstat:
	/build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram
.. ok

test_idxstat:
	/build/reproducible-path/samtools-1.21/samtools idxstats /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.sam
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck -v  /build/reproducible-path/samtools-1.21/test/quickcheck/1.quickcheck.badeof.bam /build/reproducible-path/samtools-1.21/test/quickcheck/2.quickcheck.badheader.bam /build/reproducible-path/samtools-1.21/test/quickcheck/3.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/4.quickcheck.ok.bam /build/reproducible-path/samtools-1.21/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/6.quickcheck.cram21.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/7.quickcheck.cram30.ok.cram /build/reproducible-path/samtools-1.21/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_quickcheck:
	/build/reproducible-path/samtools-1.21/samtools quickcheck -uv /build/reproducible-path/samtools-1.21/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,'
.. ok

test_reheader:
	/build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/build/reproducible-path/samtools-1.21/samtools reheader /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v21.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/build/reproducible-path/samtools-1.21/samtools reheader --in-place /build/reproducible-path/samtools-1.21/test/reheader/hdr.sam /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram && /build/reproducible-path/samtools-1.21/samtools view -h --no-PG /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.bam | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_reheader:
	/build/reproducible-path/samtools-1.21/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/reproducible-path/samtools-1.21/test/dat/view.001.tmp.v30.cram | /build/reproducible-path/samtools-1.21/samtools view -h --no-PG | perl -pe 's/	VN:.*//'
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/reproducible-path/samtools-1.21/test/addrprg/2_fixup_orphan.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/reproducible-path/samtools-1.21/test/addrprg/4_fixup_norg.sam
.. ok

test_addrprg:
	/build/reproducible-path/samtools-1.21/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/reproducible-path/samtools-1.21/test/addrprg/1_fixup.sam
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/reproducible-path/samtools-1.21/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/1_name_sort.sam -

	ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/2_bad_order.sam -

	ERR: samtools markdup: error, not in coordinate sorted order.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/3_missing_mc.sam -

	ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first.

samtools markdup: error, unable to assign pair hash key.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/4_missing_ms.sam -

	ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.

samtools markdup: error, no ms score tag. Please run samtools fixmate on file first.


.. expected failure

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/5_markdup.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -O sam -r --no-PG /build/reproducible-path/samtools-1.21/test/markdup/6_remove_dups.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/7_mark_supp_dup.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/8_optical_dup.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/9_optical_dup_qcfail.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/reproducible-path/samtools-1.21/test/markdup/10_optical_chain.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/reproducible-path/samtools-1.21/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/11_optical_dup_regex.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/reproducible-path/samtools-1.21/test/markdup/12_optical_chain_regex.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/13_optical_barcode_tag.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/14_optical_barcode_name.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/15_optical_barcode_rgx_name.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/16_optical_barcode_rgx_name_test_2.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/reproducible-path/samtools-1.21/test/markdup/17_read_group.sam -
.. ok

test_markdup:
	/build/reproducible-path/samtools-1.21/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/reproducible-path/samtools-1.21/test/markdup/18_primary_duplicate_count.sam -
.. ok

test_bedcov:
	/build/reproducible-path/samtools-1.21/samtools bedcov /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/build/reproducible-path/samtools-1.21/samtools bedcov -j /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/build/reproducible-path/samtools-1.21/samtools bedcov -g512 -G2048 /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam
.. ok

test_bedcov:
	/build/reproducible-path/samtools-1.21/samtools bedcov -c /build/reproducible-path/samtools-1.21/test/bedcov/bedcov_gG.bed /build/reproducible-path/samtools-1.21/test/bedcov/bedcov.bam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam  /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam  /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -p 5 -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%#.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -d RG -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -d an -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -d an -M 3 -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.unk.sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.%!.%. /build/reproducible-path/samtools-1.21/test/split/split.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.unk.sam  /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam
.. ok

test_split:
	/build/reproducible-path/samtools-1.21/samtools split  -@ 2 --output-fmt sam -f /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/reproducible-path/samtools-1.21/test/split/split.tmp.d_nn.0unk.sam  /build/reproducible-path/samtools-1.21/test/split/split_d_nn.sam
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/lLvf1KLWi4/longref.sam.gz
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools view -h --no-PG /tmp/lLvf1KLWi4/longref.sam.gz CHROMOSOME_I:10000000114-10000000168
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools view -h --no-PG -L /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /tmp/lLvf1KLWi4/longref.sam.gz
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools sort -O sam --no-PG -m 10M /build/reproducible-path/samtools-1.21/test/large_pos/longref_name.sam
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools merge -O sam --no-PG - /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam /build/reproducible-path/samtools-1.21/test/large_pos/longref2.sam
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools depth /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools depth -b /build/reproducible-path/samtools-1.21/test/large_pos/test.bed /build/reproducible-path/samtools-1.21/test/large_pos/longref.sam
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/lLvf1KLWi4/longref.sam.gz
.. ok

test_large_positions:
	/build/reproducible-path/samtools-1.21/samtools sort    -O sam --no-PG -n -m 10M test/large_pos/longref3.sam |
                     /build/reproducible-path/samtools-1.21/samtools fixmate -O sam --no-PG - - |
                     /build/reproducible-path/samtools-1.21/samtools sort    -O sam --no-PG -m 10M
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --original -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG  --keep-tag --output-fmt=sam --strand --both-ends -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_test_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /build/reproducible-path/samtools-1.21/test/ampliconclip/primer_counts.tsv -b /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/3_multi_ref_data.sam
.. ok

test_ampliconclip:
	/build/reproducible-path/samtools-1.21/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test2.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/4_total_hc_data.sam
.. ok

test_ampliconstats:
	/build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconclip/1_hard_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/reproducible-path/samtools-1.21/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/multi_ref.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_ampliconstats:
	/build/reproducible-path/samtools-1.21/samtools ampliconstats -@ 2 -c 0 /build/reproducible-path/samtools-1.21/test/ampliconclip/ac_test.bed /build/reproducible-path/samtools-1.21/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line'
.. ok

test_reset:
	cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset --dupflag | /build/reproducible-path/samtools-1.21/samtools view
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag < /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools view
.. ok

test_reset:
	cat /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam | /build/reproducible-path/samtools-1.21/samtools reset  --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.bam
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam /build/reproducible-path/samtools-1.21/test/dat/test_input_1_a.cram
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG	ID:samtools	PN:samtools" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG sam_to_fixed_bam /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG	ID:" | wc -l | sed 's/ //g'
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index --no-PG /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam -o /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam; grep /build/reproducible-path/samtools-1.21/test/reset/output.tmp.sam -e"@PG"
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag --reject-PG bwa_index /build/reproducible-path/samtools-1.21/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset  --dupflag /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok

test_reset:
	/build/reproducible-path/samtools-1.21/samtools reset /build/reproducible-path/samtools-1.21/test/reset/seq.sam -o /build/reproducible-path/samtools-1.21/test/reset/output
.. ok


Number of tests:
    total            .. 990
    passed           .. 946
    failed           .. 0
    expected failure .. 44
    unexpected pass  .. 0

test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg

=== Testing mpileup.reg regressions ===
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"
[W::cram_encode_aux] Missing @RG header for RG "ERR162872"

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam

Expected   passes:   120
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="mawk" ../regression.sh depth.reg

=== Testing depth.reg regressions ===

EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam

Expected   passes:   53
Unexpected passes:   0
Expected   failures: 1
Unexpected failures: 0
=> PASS
cd test/mpileup && AWK="mawk" ../regression.sh cram-size.reg

=== Testing cram-size.reg regressions ===

Expected   passes:   5
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/consensus && AWK="mawk" ../regression.sh consensus.reg

=== Testing consensus.reg regressions ===

Expected   passes:   65
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg

=== Testing cram_size.reg regressions ===

Expected   passes:   3
Unexpected passes:   0
Expected   failures: 0
Unexpected failures: 0
=> PASS
make[2]: Leaving directory '/build/reproducible-path/samtools-1.21'
	rm -fr -- /tmp/dh-xdg-rundir-xD0B56gg
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
   create-stamp debian/debhelper-build-stamp
   dh_prep
	rm -f -- debian/samtools.substvars debian/samtools-test.substvars
	rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ debian/.debhelper/generated/samtools-test/ debian/samtools-test/
	rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log
   debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
dh_auto_install -- \
  prefix=/usr
	install -m0755 -d /build/reproducible-path/samtools-1.21/debian/tmp
	make -j4 install DESTDIR=/build/reproducible-path/samtools-1.21/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
mkdir -p -m 755 /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1
install -p samtools /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin
install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin
install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /build/reproducible-path/samtools-1.21/debian/tmp/usr/bin
install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/reproducible-path/samtools-1.21/debian/tmp/usr/share/man/man1
make[2]: Leaving directory '/build/reproducible-path/samtools-1.21'
make clean
make[2]: Entering directory '/build/reproducible-path/samtools-1.21'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* *.fa.fai anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam*
cd test/reference && rm -f mpileup.*.fai
rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o
rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/build/reproducible-path/samtools-1.21'
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
	rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log
   debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
dh_install
	install -m0755 -d debian/samtools//usr
	cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
	install -m0755 -d debian/samtools//usr/share/man
	cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
	install -m0755 -d debian/samtools/usr/share/commonwl/
	cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl//
	install -m0755 -d debian/samtools/usr/share/man/man1
	cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
	install -m0755 -d debian/samtools-test/usr/share/doc/samtools
	cp --reflink=auto -a ./debian/tests/run-unit-test debian/samtools-test/usr/share/doc/samtools/
	install -m0755 -d debian/samtools-test/usr/share/samtools
	cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/
# Fix Perl interpreter PATH
for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \
    sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \
done
# Disable the executable bit on a dataset.
if [ -d debian/samtools-test ] \
; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \
; fi
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
   dh_installdocs
	install -m0755 -d debian/samtools/usr/share/doc/samtools
	install -m0755 -d debian/samtools/usr/share/doc/samtools
	cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools
	cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools
	cp --reflink=auto -a ./debian/README.test debian/samtools/usr/share/doc/samtools
	chmod -R u\+rw,go=rX debian/samtools/usr/share/doc
	install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
	install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
	install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test
	install -p -m0644 debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright
	rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log
   debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
dh_installchangelogs NEWS.md
	install -m0755 -d debian/samtools/usr/share/doc/samtools
	install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian
	install -p -m0644 NEWS.md debian/samtools/usr/share/doc/samtools/changelog
	install -m0755 -d debian/samtools-test/usr/share/doc/samtools-test
	install -p -m0644 debian/.debhelper/generated/samtools-test/dh_installchangelogs.dch.trimmed debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian
	install -p -m0644 NEWS.md debian/samtools-test/usr/share/doc/samtools-test/changelog
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
   dh_installexamples
	install -m0755 -d debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples
	cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples
	rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log
   debian/rules execute_before_dh_installman
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
# Fix whatis entries for subcommands; "samtools subcommand \- desc."
# will confuse the lexer, but "samtools-subcommand \- desc." will work.
sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \
	debian/*/usr/share/man/man*/*.*
# .EX expects a indentation width.
sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.*
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
   dh_installman
	rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
	ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
	mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1
	mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1
	mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1
	mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1
	mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1
	mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1
	mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1
	mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1
	mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1
	mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1
	mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1
	mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1
	mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1
	mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1
	mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1
	mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1
	mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1
	mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1
	mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1
	mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1
	mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1
	mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1
	mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1
	mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1
	mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1
	mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1
	mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1
	mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1
	mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1
	mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1
	mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1
	mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1
	mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1
	mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1
	mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1
	mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1
	mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1
	mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1
	mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1
	mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1
	mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1
	mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1
	mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1
	chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1
   dh_lintian
	install -m0755 -d debian/samtools/usr/share/lintian/overrides
	install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
   dh_perl
	mv debian/samtools.substvars.new debian/samtools.substvars
	mv debian/samtools-test.substvars.new debian/samtools-test.substvars
   dh_link
	rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1
	ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1
   dh_strip_nondeterminism
	Using 1731584159 as canonical time
	Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip
	Using 1731584159 as canonical time
	Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip
   dh_compress
	cd debian/samtools
	cd debian/samtools-test
	chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian
	chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
	gzip -9nf usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
	gzip -9nf usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian
	cd '/build/reproducible-path/samtools-1.21'
	cd '/build/reproducible-path/samtools-1.21'
	rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
	ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz
   dh_fixperms
	find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
   debian/rules execute_after_dh_fixperms-indep
make[1]: Entering directory '/build/reproducible-path/samtools-1.21'
chmod -x /build/reproducible-path/samtools-1.21/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam
make[1]: Leaving directory '/build/reproducible-path/samtools-1.21'
   dh_missing
   dh_dwz -a
	install -m0755 -d debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf
	dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim
dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 729158 new size 750642
	objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
	chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug
   dh_strip -a
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug
	strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/df/692591be73a860f596386f769a08d2034a2d43.debug debian/samtools/usr/bin/ace2sam
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.debug
	strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/67/e928e02c0111fee9a809fa505157999a001621.debug debian/samtools/usr/bin/maq2sam-short
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.debug
	strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/4f2a177ea7991a0822e26944c28ad098e39606.debug debian/samtools/usr/bin/maq2sam-long
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug
	strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4a/3389d400e7a3f36f8902d21b43794fc0e5302f.debug debian/samtools/usr/bin/wgsim
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug
	strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/0f3c191656ce7f7f819003dbcaa4296e2973a0.debug debian/samtools/usr/bin/md5fa
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug
	strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/ca1f475bfbcda812a638c0eeea747ea9cc5f22.debug debian/samtools/usr/bin/samtools
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d
	objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug
	strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
	objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/2a4e264350e4290193be9c8c57a1ed7add64ea.debug debian/samtools/usr/bin/md5sum-lite
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz
	rm -fr debian/samtools/usr/lib/debug/.dwz
	rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
	ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym
	install -m0755 -d debian/.debhelper/samtools
   dh_makeshlibs -a
	rm -f debian/samtools/DEBIAN/shlibs
   dh_shlibdeps -a
	install -m0755 -d debian/samtools/DEBIAN
	dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
   dh_installdeb
	install -m0755 -d debian/samtools/DEBIAN
	install -m0755 -d debian/samtools-test/DEBIAN
   dh_gencontrol
	install -m0755 -d debian/samtools-test/DEBIAN
	echo misc:Depends= >> debian/samtools-test.substvars
	echo misc:Pre-Depends= >> debian/samtools-test.substvars
	dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test
	install -m0755 -d debian/samtools/DEBIAN
	echo misc:Depends= >> debian/samtools.substvars
	echo misc:Pre-Depends= >> debian/samtools.substvars
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
	dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=144f2a177ea7991a0822e26944c28ad098e39606 48ca1f475bfbcda812a638c0eeea747ea9cc5f22 4a3389d400e7a3f36f8902d21b43794fc0e5302f 5d2a4e264350e4290193be9c8c57a1ed7add64ea 67e928e02c0111fee9a809fa505157999a001621 710f3c191656ce7f7f819003dbcaa4296e2973a0 df692591be73a860f596386f769a08d2034a2d43" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools
dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined
	chmod 0644 -- debian/samtools-test/DEBIAN/control
dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined
	chmod 0644 -- debian/samtools/DEBIAN/control
   dh_md5sums
	install -m0755 -d debian/samtools/DEBIAN
	install -m0755 -d debian/samtools-test/DEBIAN
	cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/samtools/DEBIAN/md5sums
	install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
	cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
	chmod 0644 -- debian/samtools-test/DEBIAN/md5sums
   dh_builddeb
	dpkg-deb --root-owner-group --build debian/samtools ..
	dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root ..
	dpkg-deb --root-owner-group --build debian/samtools-test ..
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.21-0+exp1_armhf.deb'.
dpkg-deb: building package 'samtools' in '../samtools_1.21-0+exp1_armhf.deb'.
dpkg-deb: building package 'samtools-test' in '../samtools-test_1.21-0+exp1_all.deb'.
 dpkg-genbuildinfo --build=binary -O../samtools_1.21-0+exp1_armhf.buildinfo
 dpkg-genchanges --build=binary -O../samtools_1.21-0+exp1_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-source: info: using options from samtools-1.21/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/20800/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/20800/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/20800 and its subdirectories
I: Current time: Sat Nov 23 07:50:07 +14 2024
I: pbuilder-time-stamp: 1732297807