sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | samtools 1.22.1-1 (amd64) Mon, 29 Jun 2026 22:04:56 +0000 | +==============================================================================+ Package: samtools Version: 1.22.1-1 Source Version: 1.22.1-1 Distribution: perl-5.44-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Mon, 29 Jun 2026 22:04:57 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup samtools_1.22.1-1 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup samtools_1.22.1-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 29 Jun 2026 22:04:57 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:3 http://deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Mon, 29 Jun 2026 22:05:05 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/samtools_1.22.1-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 29 Jun 2026 22:05:05 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.22~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.22~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/samtools-V4kjE7/resolver-pELW1u/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/samtools-V4kjE7/resolver-pELW1u/apt_archive ./ InRelease Get:2 copy:/build/samtools-V4kjE7/resolver-pELW1u/apt_archive ./ Release [609 B] Ign:3 copy:/build/samtools-V4kjE7/resolver-pELW1u/apt_archive ./ Release.gpg Get:4 copy:/build/samtools-V4kjE7/resolver-pELW1u/apt_archive ./ Sources [764 B] Get:5 copy:/build/samtools-V4kjE7/resolver-pELW1u/apt_archive ./ Packages [792 B] Fetched 2165 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sensible-utils tabix zlib1g-dev Suggested packages: gnu-standards autoconf-doc doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user liblzma-doc ncurses-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx python3:any bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales libgpm2 publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 31.6 MB/32.0 MB of archives. After this operation, 133 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 libldap-dev amd64 2.6.13+dfsg-1+b1 [308 kB] Get:2 copy:/build/samtools-V4kjE7/resolver-pELW1u/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:3 file:/srv/reprepro perl-5.44/main amd64 libio-pty-perl amd64 1:1.31-1+b1 [38.4 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20241016-3 [797 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.16.0-8 [319 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-1 [332 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-1 [820 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.2 [77.1 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:29 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-1 [2660 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.2 [933 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:39 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-3 [58.3 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-3 [40.3 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-3 [41.3 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-3 [54.1 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-3 [125 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-2 [416 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.21.0-2 [17.0 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.25.1-1+b1 [619 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-5 [102 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.2-3 [222 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.13-1 [1479 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-3 [14.0 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.69.0-1 [128 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.22.0-1 [29.8 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.3-1 [3025 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-4 [393 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b2 [372 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.21.0-2 [546 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.25-1 [56.7 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1+b2 [1784 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20251231-1+b1 [107 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.6+20251231-1+b1 [356 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.22.1+ds2-1+b2 [507 kB] Preconfiguring packages ... Fetched 31.6 MB in 0s (154 MB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 14526 files and directories currently installed.) Preparing to unpack .../00-autoconf-archive_20241016-3_all.deb ... Unpacking autoconf-archive (20241016-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package bash-completion. Preparing to unpack .../02-bash-completion_1%3a2.16.0-8_all.deb ... Unpacking bash-completion (1:2.16.0-8) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.6-1) ... Setting up libunistring-dev:amd64 (1.4.2-1) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up libkeyutils1:amd64 (1.6.3-6+b2) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-3+b2) ... Setting up bsdextrautils (2.42.2-1) ... Setting up libio-pty-perl (1:1.31-1+b1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.3+dfsg-1) ... Setting up libdebhelper-perl (14.2) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up libpkgconf7:amd64 (2.5.1-4) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up libpsl5t64:amd64 (0.22.0-1) ... Setting up libnghttp2-14:amd64 (1.69.0-1) ... Setting up libdeflate0:amd64 (1.25-1) ... Setting up gettext-base (1.0-1) ... Setting up m4 (1.4.21-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up autoconf-archive (20241016-3) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libunbound8:amd64 (1.25.1-1+b1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libgnutls-dane0t64:amd64 (3.8.13-1) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up bash-completion (1:2.16.0-8) ... Setting up libldap-dev:amd64 (2.6.13+dfsg-1+b1) ... Setting up libncurses6:amd64 (6.6+20251231-1+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1) ... Setting up libssl-dev:amd64 (3.6.3-1) ... Setting up autopoint (1.0-1) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libidn2-dev:amd64 (2.3.8-5) ... Setting up autoconf (2.73-2) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libnghttp3-dev:amd64 (1.15.0-1) ... Setting up liblzma-dev:amd64 (5.8.3-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-4) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libdeflate-dev:amd64 (1.25-1) ... Setting up tabix (1.22.1+ds2-1+b2) ... Setting up libbrotli-dev:amd64 (1.2.0-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libp11-kit-dev:amd64 (0.26.2-3) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up libncurses-dev:amd64 (6.6+20251231-1+b1) ... Setting up gettext (1.0-1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.5.4-11) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up libpsl-dev:amd64 (0.22.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-4) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl4-gnutls:amd64 (8.21.0-2) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... Setting up po-debconf (1.0.22) ... Setting up libcurl3t64-gnutls:amd64 (8.21.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.22.1-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-3) ... Setting up libkdb5-10t64:amd64 (1.22.1-3) ... Setting up debhelper (14.2) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-3) ... Setting up krb5-multidev:amd64 (1.22.1-3) ... Setting up libkrb5-dev:amd64 (1.22.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.21.0-2) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1+b2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 29 Jun 2026 22:05:11 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 29 Jun 2026 22:05:11 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.0.13-1 Package versions: apt_3.3.1 autoconf_2.73-2 autoconf-archive_20241016-3 automake_1:1.18.1-4 autopoint_1.0-1 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 bash-completion_1:2.16.0-8 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.2 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-1 gettext-base_1.0-1 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.3.2-3 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl3t64-gnutls_8.21.0-2 libcurl4-gnutls_8.21.0-2 libcurl4-gnutls-dev_8.21.0-2 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.2 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.22.1+ds2-1+b2 libhts3t64_1.22.1+ds2-1+b2 libhtscodecs2_1.6.6-1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libio-pty-perl_1:1.31-1+b1 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.0-1 libk5crypto3_1.22.1-3 libkadm5clnt-mit12_1.22.1-3 libkadm5srv-mit12_1.22.1-3 libkdb5-10t64_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5-dev_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.0-3 libldap-dev_2.6.13+dfsg-1+b1 libldap2_2.6.13+dfsg-1+b1 liblsan0_16.1.0-2 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncurses-dev_6.6+20251231-1+b1 libncurses6_6.6+20251231-1+b1 libncursesw6_6.6+20251231-1+b1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-dev_1.22.1-1 libnpth0t64_1.8-3+b2 libp11-kit-dev_0.26.2-3 libp11-kit0_0.26.2-3 libpam-modules_1.7.0-6 libpam-modules-bin_1.7.0-6 libpam-runtime_1.7.0-6 libpam0g_1.7.0-6 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc1-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.22.0-1 libpsl5t64_0.22.0-1 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssh2-1-dev_1.11.1-4 libssh2-1t64_1.11.1-4 libssl-dev_3.6.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunbound8_1.25.1-1+b1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-3+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.0.13-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1+b1 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc1-1 perl-base_5.44.0~rc1-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc1-1 pinentry-curses_1.3.2-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 sysvinit-utils_3.18-1 tabix_1.22.1+ds2-1+b2 tar_1.35+dfsg-4 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Mon, 29 Jun 2026 22:05:11 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.22.1-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/samtools Vcs-Git: https://salsa.debian.org/med-team/samtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl , libncurses-dev, libhts-dev (>= 1.22~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev Package-List: samtools deb science optional arch=any samtools-test deb science optional arch=all Checksums-Sha1: 0709b89fe86790635f2ee3b96d2c69613127abd6 5742289 samtools_1.22.1.orig.tar.gz 5b0cf4c258c2541fa4a26b8e0ec9a7a2722a4733 22116 samtools_1.22.1-1.debian.tar.xz Checksums-Sha256: 55d233093fb831ea8b95b538de907f37be78862163029e7e91ab713e4744a208 5742289 samtools_1.22.1.orig.tar.gz b978ee6553de42b277b35e5e7254d795429422dc02daf608c6e0dcf7cd945071 22116 samtools_1.22.1-1.debian.tar.xz Files: c6140e6437d2cdea09b0e8dc195103c5 5742289 samtools_1.22.1.orig.tar.gz 2dcee5acb7ac69bf04c39008cc3c3875 22116 samtools_1.22.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEE3z4uQkp+J5wuSwI6ucKa7rL0UKcFAmiiQC8ACgkQucKa7rL0 UKd6MBAAhhACt4mdHsyiMGXbAInHdFNVLLmemPqteu2ZMCFEDHorn0ltC+l77Azb 5ITIfQjAiViQEOl+EE5KOVtTd09S7dJHEdhGW9byXAUpD40yROU3hATPyguVEMWi xbTjZoBkcgj3KZ5CCrU48W3yURVLN1wp3jZ4TwxFx5rV4soo2DQU75B3PxPt/Fae suWAUDCxFoVxczYDgtI1WkjA1q66TMOJJQIATKQO3UPV99rqxAIR5tOD8M9GM32p R/kaReKIGTk54srkGveg1HU3tjfrQm3NBDiFzJt7m2kLQXWje7cU7UXJ4WKVhdmE cj5Rnuk/JAr3e+bD/XQ+RUwcDXyH5jfRp341RPLJS/7v9muJnjmDrDEnD948gEcz Zguq0wA7ZclqIrAsGNjGGSTFC3nYZgrtj5AJJeOSPVk+J7pJBh/fr2XVkwEeIhGR eSLqhevS/5LFoz6lP1VPC45p2hidCIEamome+ZkNNjrxhOINsktLaiclI85gg3hT 7t3vzAk3Ek5ToETBeR1IV+9JbwDXLotW6vh+27bLFh9Bfh6xAs814nG0fCmm65Zx eh9kRbJCCc6OzCkiuHhO19x5uClSxRJUB2ZH5zKVWbQdPoLrzoN3p09gPKUK1reB hM3lsjzWxCDcYGozFD+JLilm9YA90MaZFk6nG7k3SezqBd6yzSQ= =urW3 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./samtools_1.22.1-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./samtools_1.22.1-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting samtools in /build/samtools-V4kjE7/samtools-1.22.1 dpkg-source: info: unpacking samtools_1.22.1.orig.tar.gz dpkg-source: info: unpacking samtools_1.22.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Mon, 29 Jun 2026 22:05:12 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network samtools_1.22.1-1 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network samtools_1.22.1-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/samtools-V4kjE7/samtools-1.22.1 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-ae238079-3508-4671-a11f-f24ee2558ebd SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.22.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1' rm -f config.mk touch config.mk dh_auto_clean -- make -j2 distclean make[2]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/consensus && rm -f *.bam *.bam.csi 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/samtools-V4kjE7/samtools-1.22.1' make[1]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' 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 {} + \) \) dpkg-source -Zxz -b . dpkg-source: info: using options from /build/samtools-V4kjE7/samtools-1.22.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building samtools using existing ../samtools_1.22.1.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building samtools in ../samtools_1.22.1-1.debian.tar.xz dpkg-source: info: building samtools in ../samtools_1.22.1-1.dsc 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 -v autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: subdirectory $HTSDIR not present autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1100: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level autoreconf: running: /usr/bin/autoheader --force autoreconf: configure.ac: not using Automake autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' 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/samtools-V4kjE7/samtools-1.22.1' 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.m4:1100: 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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... x86_64-linux-gnu-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 x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for x86_64-linux-gnu-gcc option to support large files... 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/samtools-V4kjE7/samtools-1.22.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j2 CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" CPPFLAGS="\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 "1.22.1"' > version.h echo '#define SAMTOOLS_CC "x86_64-linux-gnu-gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"' >> 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/samtools-V4kjE7/samtools-1.22.1@«BUILDPATH»@g' version.h x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_checksum.o bam_checksum.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMAQ_LONGREADS -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/samtools-V4kjE7/samtools-1.22.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -I./lz4 -frelease -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 x86_64-linux-gnu-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz x86_64-linux-gnu-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz x86_64-linux-gnu-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz x86_64-linux-gnu-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-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 x86_64-linux-gnu-gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread x86_64-linux-gnu-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 bam_checksum.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread x86_64-linux-gnu-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 make[2]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' make[1]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j2 test TESTSUITEFLAGS="-j2 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' 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/samtools-V4kjE7/samtools-1.22.1/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-V4kjE7/samtools-1.22.1/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-V4kjE7/samtools-1.22.1/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-V4kjE7/samtools-1.22.1/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-V4kjE7/samtools-1.22.1/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-V4kjE7/samtools-1.22.1/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-V4kjE7/samtools-1.22.1/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /build/samtools-V4kjE7/samtools-1.22.1/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/DhJl7M3mal/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/DhJl7M3mal/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/DhJl7M3mal/bgzip.dat.gz .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa 3:11-13 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa 2:998-1003 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa 1:100-104 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools faidx /tmp/DhJl7M3mal/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq 3:11-13 .. ok .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq.gz 3:11-13 .. ok .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq 2:998-1003 .. ok .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq.gz 2:998-1003 .. ok .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq 1:100-104 .. ok .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq.gz 1:100-104 .. ok .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq 1:99998-100007 .. ok .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools fqidx /tmp/DhJl7M3mal/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /build/samtools-V4kjE7/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /build/samtools-V4kjE7/samtools-1.22.1/test/dat/dict.fa .. ok test_dict: /build/samtools-V4kjE7/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/DhJl7M3mal/dict.fa.gz .. ok test_dict: cat /build/samtools-V4kjE7/samtools-1.22.1/test/dat/dict.fa | /build/samtools-V4kjE7/samtools-1.22.1/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /build/samtools-V4kjE7/samtools-1.22.1/samtools dict -AH < /build/samtools-V4kjE7/samtools-1.22.1/test/dat/dict.alias.fa .. ok test_dict: /build/samtools-V4kjE7/samtools-1.22.1/samtools dict -H -l /build/samtools-V4kjE7/samtools-1.22.1/test/dat/dict.alt < /build/samtools-V4kjE7/samtools-1.22.1/test/dat/dict.alias.fa .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view /tmp/DhJl7M3mal/large_chrom.bam ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view /tmp/DhJl7M3mal/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam && cat /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/DhJl7M3mal/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/DhJl7M3mal/test_input_1_b.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -O sam - -X -cp -R ref2 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam.bai /tmp/DhJl7M3mal/test_input_1_b.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/DhJl7M3mal/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam && cat /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -c /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam /tmp/DhJl7M3mal/auto_indexed.csi && cat /tmp/DhJl7M3mal/auto_indexed.csi .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.cram /tmp/DhJl7M3mal/auto_indexed.crai && cat /tmp/DhJl7M3mal/auto_indexed.crai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -c /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.sam /tmp/DhJl7M3mal/auto_indexed.csi && cat /tmp/DhJl7M3mal/auto_indexed.csi .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -@ 2 /tmp/DhJl7M3mal/large_chrom.bam ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -@ 2 /tmp/DhJl7M3mal/large_chrom.bam ref2:1-541556283 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -@ 2 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam && cat /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -@ 2 -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/DhJl7M3mal/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -@ 2 -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/DhJl7M3mal/test_input_1_b.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -O sam - -X -cp -R ref2 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam.bai /tmp/DhJl7M3mal/test_input_1_b.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -@ 2 -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /tmp/DhJl7M3mal/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -@ 2 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -@ 2 -M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam && cat /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam.bai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -@ 2 -X /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -@ 2 -c /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam /tmp/DhJl7M3mal/auto_indexed.csi && cat /tmp/DhJl7M3mal/auto_indexed.csi .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -@ 2 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.cram /tmp/DhJl7M3mal/auto_indexed.crai && cat /tmp/DhJl7M3mal/auto_indexed.crai .. ok test_index: /build/samtools-V4kjE7/samtools-1.22.1/samtools index -@ 2 -c /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.sam /tmp/DhJl7M3mal/auto_indexed.csi && cat /tmp/DhJl7M3mal/auto_indexed.csi .. ok test_mpileup: /build/samtools-V4kjE7/samtools-1.22.1/samtools mpileup -b /tmp/DhJl7M3mal/mpileup.bam.list -f /tmp/DhJl7M3mal/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-V4kjE7/samtools-1.22.1/samtools mpileup -b /tmp/DhJl7M3mal/mpileup.cram.list -f /tmp/DhJl7M3mal/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-V4kjE7/samtools-1.22.1/samtools mpileup -b /tmp/DhJl7M3mal/mpileup.bam.urllist -f /tmp/DhJl7M3mal/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-V4kjE7/samtools-1.22.1/samtools mpileup -b /tmp/DhJl7M3mal/mpileup.cram.urllist -f /tmp/DhJl7M3mal/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /build/samtools-V4kjE7/samtools-1.22.1/samtools mpileup -B --ff 0x14 -f /tmp/DhJl7M3mal/mpileup.ref.fa.gz -r17:1050-1060 /tmp/DhJl7M3mal/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /build/samtools-V4kjE7/samtools-1.22.1/samtools mpileup -B --ff 0x14 -f /tmp/DhJl7M3mal/mpileup.ref.fa.gz -r17:1050-1060 /tmp/DhJl7M3mal/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /build/samtools-V4kjE7/samtools-1.22.1/samtools mpileup /build/samtools-V4kjE7/samtools-1.22.1/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, checksum, 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 checksum Usage on stderr rather than stdout .. expected failure 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/DhJl7M3mal/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/DhJl7M3mal/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/DhJl7M3mal/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/DhJl7M3mal/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/DhJl7M3mal/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/DhJl7M3mal/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/DhJl7M3mal/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/DhJl7M3mal/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/DhJl7M3mal/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/DhJl7M3mal/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/DhJl7M3mal/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/DhJl7M3mal/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/DhJl7M3mal/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/DhJl7M3mal/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/DhJl7M3mal/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/DhJl7M3mal/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/DhJl7M3mal/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/DhJl7M3mal/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/DhJl7M3mal/view.001.forn (SAM input) .. ok 68: Count -N /tmp/DhJl7M3mal/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/DhJl7M3mal/view.001.forn (BAM input) .. ok 70: Count -N /tmp/DhJl7M3mal/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/DhJl7M3mal/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/DhJl7M3mal/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/DhJl7M3mal/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/DhJl7M3mal/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/DhJl7M3mal/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/DhJl7M3mal/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/DhJl7M3mal/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/DhJl7M3mal/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/DhJl7M3mal/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/DhJl7M3mal/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/DhJl7M3mal/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/DhJl7M3mal/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/DhJl7M3mal/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/DhJl7M3mal/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/DhJl7M3mal/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/DhJl7M3mal/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/DhJl7M3mal/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/DhJl7M3mal/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/DhJl7M3mal/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/DhJl7M3mal/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/DhJl7M3mal/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/DhJl7M3mal/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/DhJl7M3mal/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/DhJl7M3mal/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/DhJl7M3mal/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test115.sam -h -d TGCA /tmp/DhJl7M3mal/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -c -d TGCA /tmp/DhJl7M3mal/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test117.sam -h -d TGCA /tmp/DhJl7M3mal/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -c -d TGCA /tmp/DhJl7M3mal/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test119.sam -h -d TGCA /tmp/DhJl7M3mal/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -c -d TGCA /tmp/DhJl7M3mal/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/DhJl7M3mal/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/DhJl7M3mal/view.001.fobc" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test121.sam -h -D BClong:/tmp/DhJl7M3mal/view.001.fobc /tmp/DhJl7M3mal/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/DhJl7M3mal/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/DhJl7M3mal/view.001.fobc" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -c -D BClong:/tmp/DhJl7M3mal/view.001.fobc /tmp/DhJl7M3mal/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/DhJl7M3mal/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/DhJl7M3mal/view.001.fobc" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test123.sam -h -D BClong:/tmp/DhJl7M3mal/view.001.fobc /tmp/DhJl7M3mal/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/DhJl7M3mal/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/DhJl7M3mal/view.001.fobc" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -c -D BClong:/tmp/DhJl7M3mal/view.001.fobc /tmp/DhJl7M3mal/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/DhJl7M3mal/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/DhJl7M3mal/view.001.fobc" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test125.sam -h -D BClong:/tmp/DhJl7M3mal/view.001.fobc /tmp/DhJl7M3mal/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/DhJl7M3mal/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/DhJl7M3mal/view.001.fobc" Failed command: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -c -D BClong:/tmp/DhJl7M3mal/view.001.fobc /tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/samtools view -o /tmp/DhJl7M3mal/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/DhJl7M3mal/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/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools head /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -h 0 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -h 1 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -h 5 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -h 29 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -h 30 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -n 0 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -n 1 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -n 5 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.sam .. ok test_head: /build/samtools-V4kjE7/samtools-1.22.1/samtools head -h 5 -n 5 < /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -0 /build/samtools-V4kjE7/samtools-1.22.1/test/0.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -0 /build/samtools-V4kjE7/samtools-1.22.1/test/0.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -i --index-format 'i*i*' -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -T RG,BC,QT -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -T RG,BC,QT,MD,ia -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools fastq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc_split.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -t -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -t -T MD,ia -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/i.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/i.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -i --index-format 'i*i*' -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -1 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fasta -N -1 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fa -2 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fa /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -o /build/samtools-V4kjE7/samtools-1.22.1/test/o.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -s /tmp/DhJl7M3mal/bam2fq.discard.s.fq -0 /tmp/DhJl7M3mal/bam2fq.discard.0.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -T ba,bb,bc,bd,be,bf,bg /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq --index-format 'i8n1i8' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/i1.fq --i2 /build/samtools-V4kjE7/samtools-1.22.1/test/i2.fq -0 /build/samtools-V4kjE7/samtools-1.22.1/test/0.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -T '' /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -t -T '*' /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -T '*' -d MD:10 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -T '*' -d NM:0 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -N -T '*' -d ia /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -d NM:13 -d NM:14 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -D NM:test/dat/bam2fq.NM-D /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -D MD:test/dat/bam2fq.MD-D /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.002.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.003.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.010.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/bc_split.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -t -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -t -T MD,ia -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/i.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.004.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/i.fq -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -i --index-format 'i*i*' -s /build/samtools-V4kjE7/samtools-1.22.1/test/s.fq -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.005.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -1 /build/samtools-V4kjE7/samtools-1.22.1/test/1.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/2.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.703.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -1 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fq -2 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fasta -@ 2 -N -1 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fa -2 /build/samtools-V4kjE7/samtools-1.22.1/test/o.fa /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -o /build/samtools-V4kjE7/samtools-1.22.1/test/o.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -s /tmp/DhJl7M3mal/bam2fq.discard.s.fq -0 /tmp/DhJl7M3mal/bam2fq.discard.0.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.013.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /build/samtools-V4kjE7/samtools-1.22.1/test/i1.fq --i2 /build/samtools-V4kjE7/samtools-1.22.1/test/i2.fq -0 /build/samtools-V4kjE7/samtools-1.22.1/test/0.fq /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.014.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -T '' /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -t -T '*' /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d MD:10 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d NM:0 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -N -T '*' -d ia /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -d NM:13 -d NM:14 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /build/samtools-V4kjE7/samtools-1.22.1/test/dat/bam2fq.001.sam .. ok test_bam2fq: /build/samtools-V4kjE7/samtools-1.22.1/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa -i 0 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -S RG -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -S RG -r /build/samtools-V4kjE7/samtools-1.22.1/test/stat/test.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -t /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11.stats.targets /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -g 4 -t /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11.stats.targets /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -g 4 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_overlaps.bam -t /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_overlaps.bam -p -t /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_overlaps.bam -t /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_overlaps.bam -p -t /build/samtools-V4kjE7/samtools-1.22.1/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -I s1 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -I grp2 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -I grp3 /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -I Sample /build/samtools-V4kjE7/samtools-1.22.1/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /build/samtools-V4kjE7/samtools-1.22.1/samtools stats -r /build/samtools-V4kjE7/samtools-1.22.1/test/mpileup/ce.fa /build/samtools-V4kjE7/samtools-1.22.1/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -s 1 -O sam -b /tmp/xlwGNMNkAP - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -r -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -cp -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a_regex.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -o - -s 1 -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/DhJl7M3mal/merge.tag.1.bam /tmp/DhJl7M3mal/merge.tag.2.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/DhJl7M3mal/merge.tag.3.bam /tmp/DhJl7M3mal/merge.tag.4.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge --no-PG -O SAM - /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge --no-PG -O SAM -L /build/samtools-V4kjE7/samtools-1.22.1/test/merge/merge.bed - /tmp/DhJl7M3mal/merge.bed.1.bam /tmp/DhJl7M3mal/merge.bed.2.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge --no-PG -r -O SAM - /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge --no-PG -O SAM --template-coordinate - /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_template_coordinate.1.sam /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_template_coordinate.2.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam -b /tmp/BcQuazSYTr - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -r -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -cp -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -s 1 -O sam - /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a_regex.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b_regex.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -o - -s 1 -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_c.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/DhJl7M3mal/merge.tag.1.bam /tmp/DhJl7M3mal/merge.tag.2.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/DhJl7M3mal/merge.tag.3.bam /tmp/DhJl7M3mal/merge.tag.4.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM - /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM -L /build/samtools-V4kjE7/samtools-1.22.1/test/merge/merge.bed - /tmp/DhJl7M3mal/merge.bed.1.bam /tmp/DhJl7M3mal/merge.bed.2.bam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 --no-PG -r -O SAM - /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -@ 2 --no-PG -O SAM --template-coordinate - /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_template_coordinate.1.sam /build/samtools-V4kjE7/samtools-1.22.1/test/merge/test_template_coordinate.2.sam .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/DhJl7M3mal/sortout .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -f /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/DhJl7M3mal/sortout.bam .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -o /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/DhJl7M3mal/sorttmp .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -n -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -N -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -n -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -t RG -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -n -t RG -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -t AS -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -t FI -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort --template-coordinate -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -m 10M -M -K10 -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -m 10M -M -K10 -I /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -m 10M -MH -K10 -I /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/DhJl7M3mal/sortout .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -f /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/DhJl7M3mal/sortout.bam .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -o /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam /tmp/DhJl7M3mal/sorttmp .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -n -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -N -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -n -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -t RG -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -n -t RG -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -t AS -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -t FI -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 --template-coordinate -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -m 10M -M -K10 -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -m 10M -M -K10 -I /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/dat/auto_indexed.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -@ 2 -m 10M -MH -K10 -I /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate --output-fmt=sam -O /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate1.tmp.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate2.tmp.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate2.tmp .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate --output-fmt=sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate3.tmp .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate --output-fmt=sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/collate/fast_collate.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate --output-fmt=sam -f -r 4 /build/samtools-V4kjE7/samtools-1.22.1/test/collate/fast_collate.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -O /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -@ 2 -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate1.tmp.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -@ 2 -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate2.tmp.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate2.tmp .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_d.sam /build/samtools-V4kjE7/samtools-1.22.1/test/collate/collate3.tmp .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/collate/fast_collate.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/1_fast_collate.sam .. ok test_collate: /build/samtools-V4kjE7/samtools-1.22.1/samtools collate -@ 2 --output-fmt=sam -f -r 4 /build/samtools-V4kjE7/samtools-1.22.1/test/collate/fast_collate.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -cO sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -cO sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -cO sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/5_ct.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -cO sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/sanitize.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_draft.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -@ 2 -M -z off -O sam /build/samtools-V4kjE7/samtools-1.22.1/test/fixmate/mod_bounds.sam - .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools calmd -uAr /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.ref.fa .. ok /build/samtools-V4kjE7/samtools-1.22.1/samtools calmd -@ 2 -uAr /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.ref.fa .. ok test_idxstat: /build/samtools-V4kjE7/samtools-1.22.1/samtools idxstats /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_idxstat: /build/samtools-V4kjE7/samtools-1.22.1/samtools idxstats /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.cram .. ok test_idxstat: /build/samtools-V4kjE7/samtools-1.22.1/samtools idxstats /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.sam .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck -v /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/1.quickcheck.badeof.bam /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/2.quickcheck.badheader.bam /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/3.quickcheck.ok.bam /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/4.quickcheck.ok.bam /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/5.quickcheck.scramble30.truncated.cram /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/6.quickcheck.cram21.ok.cram /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/7.quickcheck.cram30.ok.cram /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/8.quickcheck.cram21.truncated.cram /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/9.quickcheck.cram30.truncated.cram /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /build/samtools-V4kjE7/samtools-1.22.1/samtools quickcheck -uv /build/samtools-V4kjE7/samtools-1.22.1/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /build/samtools-V4kjE7/samtools-1.22.1/samtools reheader /build/samtools-V4kjE7/samtools-1.22.1/test/reheader/hdr.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-V4kjE7/samtools-1.22.1/samtools reheader /build/samtools-V4kjE7/samtools-1.22.1/test/reheader/hdr.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.v21.cram | /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-V4kjE7/samtools-1.22.1/samtools reheader /build/samtools-V4kjE7/samtools-1.22.1/test/reheader/hdr.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-V4kjE7/samtools-1.22.1/samtools reheader --in-place /build/samtools-V4kjE7/samtools-1.22.1/test/reheader/hdr.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.v21.cram && /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-V4kjE7/samtools-1.22.1/samtools reheader --in-place /build/samtools-V4kjE7/samtools-1.22.1/test/reheader/hdr.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.v30.cram && /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-V4kjE7/samtools-1.22.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.bam | /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /build/samtools-V4kjE7/samtools-1.22.1/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /build/samtools-V4kjE7/samtools-1.22.1/test/dat/view.001.tmp.v30.cram | /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -O sam -m overwrite_all /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -O sam -m orphan_only /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -O sam -R '1#9' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m orphan_only /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -R '1#9' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /build/samtools-V4kjE7/samtools-1.22.1/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /build/samtools-V4kjE7/samtools-1.22.1/test/addrprg/1_fixup.sam .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools markdup -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools markdup -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -O sam -r --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/17_read_group.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/5_markdup.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -O sam -r --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/6_remove_dups.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/8_optical_dup.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/10_optical_chain.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/17_read_group.sam - .. ok test_markdup: /build/samtools-V4kjE7/samtools-1.22.1/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /build/samtools-V4kjE7/samtools-1.22.1/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /build/samtools-V4kjE7/samtools-1.22.1/samtools bedcov /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov.bed /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-V4kjE7/samtools-1.22.1/samtools bedcov -j /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov.bed /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-V4kjE7/samtools-1.22.1/samtools bedcov -g512 -G2048 /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov_gG.bed /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov.bam .. ok test_bedcov: /build/samtools-V4kjE7/samtools-1.22.1/samtools bedcov -c /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov_gG.bed /build/samtools-V4kjE7/samtools-1.22.1/test/bedcov/bedcov.bam .. ok .. ok .. ok .. ok .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%#.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -p 5 -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%#.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -d RG -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -d an -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -d an -M 3 -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.unk.sam /build/samtools-V4kjE7/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split --output-fmt sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.0unk.sam /build/samtools-V4kjE7/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%#.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -p 5 -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%#.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d RG -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d an -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.unk.sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.%!.%. /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -d nn -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.unk.sam /build/samtools-V4kjE7/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_split: /build/samtools-V4kjE7/samtools-1.22.1/samtools split -@ 2 --output-fmt sam -f /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /build/samtools-V4kjE7/samtools-1.22.1/test/split/split.tmp.d_nn.0unk.sam /build/samtools-V4kjE7/samtools-1.22.1/test/split/split_d_nn.sam .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG /tmp/DhJl7M3mal/longref.sam.gz .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG /tmp/DhJl7M3mal/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools view -h --no-PG -L /build/samtools-V4kjE7/samtools-1.22.1/test/large_pos/test.bed /tmp/DhJl7M3mal/longref.sam.gz .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -O sam --no-PG -m 10M /build/samtools-V4kjE7/samtools-1.22.1/test/large_pos/longref_name.sam .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools merge -O sam --no-PG - /build/samtools-V4kjE7/samtools-1.22.1/test/large_pos/longref.sam /build/samtools-V4kjE7/samtools-1.22.1/test/large_pos/longref2.sam .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools depth /build/samtools-V4kjE7/samtools-1.22.1/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools depth -b /build/samtools-V4kjE7/samtools-1.22.1/test/large_pos/test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/large_pos/longref.sam .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/DhJl7M3mal/longref.sam.gz .. ok test_large_positions: /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /build/samtools-V4kjE7/samtools-1.22.1/samtools fixmate -O sam --no-PG - - | /build/samtools-V4kjE7/samtools-1.22.1/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --primer-counts /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam --keep-tag --primer-counts /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test2.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --primer-counts /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/primer_counts.tsv --output-fmt=sam -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --primer-counts /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --keep-tag --primer-counts /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/primer_counts.tsv -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/3_multi_ref_data.sam .. ok test_ampliconclip: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test2.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_hard_clipped.expected.sam /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_soft_clipped.expected.sam /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/1_soft_clipped_strand.expected.sam /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconstats -@ 2 -c 0 /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/multi_ref.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /build/samtools-V4kjE7/samtools-1.22.1/samtools ampliconstats -@ 2 -c 0 /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconclip/ac_test.bed /build/samtools-V4kjE7/samtools-1.22.1/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam | /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag | /build/samtools-V4kjE7/samtools-1.22.1/samtools view .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag < /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam | /build/samtools-V4kjE7/samtools-1.22.1/samtools view .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam | /build/samtools-V4kjE7/samtools-1.22.1/samtools view .. ok test_reset: cat /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam | /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.bam .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/test_input_1_a.cram .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG sam_to_fixed_bam /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index --no-PG /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam; grep /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag --reject-PG bwa_index /build/samtools-V4kjE7/samtools-1.22.1/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset --dupflag /build/samtools-V4kjE7/samtools-1.22.1/test/reset/seq.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_reset: /build/samtools-V4kjE7/samtools-1.22.1/samtools reset /build/samtools-V4kjE7/samtools-1.22.1/test/reset/seq.sam -o /build/samtools-V4kjE7/samtools-1.22.1/test/reset/output .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -a /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -qv /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -qv -a /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -m /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -m /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -@ 2 /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk1.bam | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -@ 2 /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -@ 2 -a /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -@ 2 -qv /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -@ 2 -qv -a /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2.cram | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -@ 2 -m /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk1-ERR*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok test_checksum: /build/samtools-V4kjE7/samtools-1.22.1/samtools checksum -@ 2 -m /build/samtools-V4kjE7/samtools-1.22.1/test/checksum/chk2-*.tmp.chk | sed 's/\(# Checksum[^:]*:\).*/\1/' .. ok Number of tests: total .. 1009 passed .. 964 failed .. 0 expected failure .. 45 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: 55 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: 77 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" PARAM="-@4 -Z4" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 77 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/samtools-V4kjE7/samtools-1.22.1' rm -fr -- /tmp/dh-xdg-rundir-TLhdg_wV make[1]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' 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/samtools-V4kjE7/samtools-1.22.1' dh_auto_install -- \ prefix=/usr install -m0755 -d /build/samtools-V4kjE7/samtools-1.22.1/debian/tmp make -j2 install DESTDIR=/build/samtools-V4kjE7/samtools-1.22.1/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' mkdir -p -m 755 /build/samtools-V4kjE7/samtools-1.22.1/debian/tmp/usr/bin /build/samtools-V4kjE7/samtools-1.22.1/debian/tmp/usr/bin /build/samtools-V4kjE7/samtools-1.22.1/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-V4kjE7/samtools-1.22.1/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/samtools-V4kjE7/samtools-1.22.1/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/samtools-V4kjE7/samtools-1.22.1/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/samtools-V4kjE7/samtools-1.22.1/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' make clean make[2]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/consensus && rm -f *.bam *.bam.csi 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/samtools-V4kjE7/samtools-1.22.1' make[1]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' 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/samtools-V4kjE7/samtools-1.22.1' 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/samtools-V4kjE7/samtools-1.22.1' dh_installchangelogs NEWS.md 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 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 make[1]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' 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/samtools-V4kjE7/samtools-1.22.1' # 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/samtools-V4kjE7/samtools-1.22.1' 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-checksum.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 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 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 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 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/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-checksum.1.dh-new debian/samtools/usr/share/man/man1/samtools-checksum.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 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 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-checksum.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 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 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.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 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-idxstats.1 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 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 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 1755458966 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1755458966 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/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-checksum.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 chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian 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-checksum.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/samtools-V4kjE7/samtools-1.22.1' cd '/build/samtools-V4kjE7/samtools-1.22.1' 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/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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 debian/rules execute_after_dh_fixperms-indep make[1]: Entering directory '/build/samtools-V4kjE7/samtools-1.22.1' chmod -x /build/samtools-V4kjE7/samtools-1.22.1/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam make[1]: Leaving directory '/build/samtools-V4kjE7/samtools-1.22.1' dh_missing dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/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 860768 new size 885001 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug dh_strip -a install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/8d5a88a699fa7871a7cd81017cd130230bd59d.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/8d5a88a699fa7871a7cd81017cd130230bd59d.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/9c/8d5a88a699fa7871a7cd81017cd130230bd59d.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f8 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f8/fbebab34efdd0b251496d87b983f628b01e768.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f8/fbebab34efdd0b251496d87b983f628b01e768.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/f8/fbebab34efdd0b251496d87b983f628b01e768.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/26 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/26/aab163c045d5a8e3481d0becdf6f2779ada204.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/26/aab163c045d5a8e3481d0becdf6f2779ada204.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/26/aab163c045d5a8e3481d0becdf6f2779ada204.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ff objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ff/d238be4a1087644896aee9c8eabafb518b870c.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ff/d238be4a1087644896aee9c8eabafb518b870c.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/ff/d238be4a1087644896aee9c8eabafb518b870c.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e0 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e0/71c9beb94795fb589405278723f925d8c73765.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e0/71c9beb94795fb589405278723f925d8c73765.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/e0/71c9beb94795fb589405278723f925d8c73765.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5c/696ec446ab91568f48396e7e66fa39c5ddf55c.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5c/696ec446ab91568f48396e7e66fa39c5ddf55c.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/5c/696ec446ab91568f48396e7e66fa39c5ddf55c.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/01 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/01/2a06cec95aaad10bf8489fa4f1e057997d5431.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/01/2a06cec95aaad10bf8489fa4f1e057997d5431.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/01/2a06cec95aaad10bf8489fa4f1e057997d5431.debug debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/x86_64-linux-gnu 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/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long dh_installdeb install -m0755 -d debian/samtools/DEBIAN install -m0755 -d debian/samtools-test/DEBIAN dh_gencontrol 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="012a06cec95aaad10bf8489fa4f1e057997d5431 26aab163c045d5a8e3481d0becdf6f2779ada204 5c696ec446ab91568f48396e7e66fa39c5ddf55c 9c8d5a88a699fa7871a7cd81017cd130230bd59d e071c9beb94795fb589405278723f925d8c73765 f8fbebab34efdd0b251496d87b983f628b01e768 ffd238be4a1087644896aee9c8eabafb518b870c" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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 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 ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/samtools-test/DEBIAN cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools' in '../samtools_1.22.1-1_amd64.deb'. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.22.1-1_all.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.22.1-1_amd64.deb'. dpkg-genbuildinfo -O../samtools_1.22.1-1_amd64.buildinfo dpkg-genchanges -O../samtools_1.22.1-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from /build/samtools-V4kjE7/samtools-1.22.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2026-06-29T22:06:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 29 Jun 2026 22:06:21 +0000 | +------------------------------------------------------------------------------+ samtools_1.22.1-1_amd64.changes: -------------------------------- Format: 1.8 Date: Sun, 17 Aug 2025 21:29:26 +0200 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: source amd64 all Version: 1.22.1-1 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats samtools-test - test files for the samtools package Changes: samtools (1.22.1-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.7.2 (routine-update) Checksums-Sha1: b8f63db026c92ea9566efdfc7ad5a81f6795746e 1383 samtools_1.22.1-1.dsc 0709b89fe86790635f2ee3b96d2c69613127abd6 5742289 samtools_1.22.1.orig.tar.gz ae367462c8785b6dff5b4c0d16ae8bb4852ea068 22120 samtools_1.22.1-1.debian.tar.xz 6e9904124397cf12089430aa480e5335fd78d921 1057300 samtools-dbgsym_1.22.1-1_amd64.deb b26f0a6c2b01aa390a5619ea21f98c10ccbb2a21 2388504 samtools-test_1.22.1-1_all.deb e3fb7b0a6f64527b457be7f5f8e4fccf1f80cf89 7739 samtools_1.22.1-1_amd64.buildinfo 8668230c2dc8ad05ab7182ff1ef22988bb0d49e0 697968 samtools_1.22.1-1_amd64.deb Checksums-Sha256: 3ff6633d5646044c847c832d3a0a14d8285b071699d0b0236a6dca0fb0ec373d 1383 samtools_1.22.1-1.dsc 55d233093fb831ea8b95b538de907f37be78862163029e7e91ab713e4744a208 5742289 samtools_1.22.1.orig.tar.gz f0765751c0c7c7d2a6172da6fb8a16f58fff5a47afc1a74b08725646d370a6ac 22120 samtools_1.22.1-1.debian.tar.xz 27e53eca778da9922b016d2b0c3c736c22a9c40e5367a6eab2558b113e77b68c 1057300 samtools-dbgsym_1.22.1-1_amd64.deb 9ea65d12e01686507a813cdbddade250373a4ecf9aa662727a89f7adc5323569 2388504 samtools-test_1.22.1-1_all.deb b9858aae90764bc679f9f0f480dfc7f46bf58e6b681c5bd0814ee45aff1d283e 7739 samtools_1.22.1-1_amd64.buildinfo 59388e4d032f24967790f1b9915628fac026d797dac79d8a710db408f54ee855 697968 samtools_1.22.1-1_amd64.deb Files: c96d2d830205c6de50933a5e8a749ca7 1383 science optional samtools_1.22.1-1.dsc c6140e6437d2cdea09b0e8dc195103c5 5742289 science optional samtools_1.22.1.orig.tar.gz 6698a2094ca97155ad0671bd79592969 22120 science optional samtools_1.22.1-1.debian.tar.xz 445bf1e29ec130f77df23d638f069089 1057300 debug optional samtools-dbgsym_1.22.1-1_amd64.deb be82cbf90221b013c8fa6ae2049bc287 2388504 science optional samtools-test_1.22.1-1_all.deb 79b7b27583c574c3f8b4938a5ab1ee01 7739 science optional samtools_1.22.1-1_amd64.buildinfo 3c099e17a9cd992c6b68a28120dc4fba 697968 science optional samtools_1.22.1-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 29 Jun 2026 22:06:21 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: all amd64 source Version: 1.22.1-1 Checksums-Md5: c96d2d830205c6de50933a5e8a749ca7 1383 samtools_1.22.1-1.dsc 445bf1e29ec130f77df23d638f069089 1057300 samtools-dbgsym_1.22.1-1_amd64.deb be82cbf90221b013c8fa6ae2049bc287 2388504 samtools-test_1.22.1-1_all.deb 3c099e17a9cd992c6b68a28120dc4fba 697968 samtools_1.22.1-1_amd64.deb Checksums-Sha1: b8f63db026c92ea9566efdfc7ad5a81f6795746e 1383 samtools_1.22.1-1.dsc 6e9904124397cf12089430aa480e5335fd78d921 1057300 samtools-dbgsym_1.22.1-1_amd64.deb b26f0a6c2b01aa390a5619ea21f98c10ccbb2a21 2388504 samtools-test_1.22.1-1_all.deb 8668230c2dc8ad05ab7182ff1ef22988bb0d49e0 697968 samtools_1.22.1-1_amd64.deb Checksums-Sha256: 3ff6633d5646044c847c832d3a0a14d8285b071699d0b0236a6dca0fb0ec373d 1383 samtools_1.22.1-1.dsc 27e53eca778da9922b016d2b0c3c736c22a9c40e5367a6eab2558b113e77b68c 1057300 samtools-dbgsym_1.22.1-1_amd64.deb 9ea65d12e01686507a813cdbddade250373a4ecf9aa662727a89f7adc5323569 2388504 samtools-test_1.22.1-1_all.deb 59388e4d032f24967790f1b9915628fac026d797dac79d8a710db408f54ee855 697968 samtools_1.22.1-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 29 Jun 2026 22:06:20 +0000 Build-Path: /build/samtools-V4kjE7/samtools-1.22.1 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), autoconf-archive (= 20241016-3), automake (= 1:1.18.1-4), autopoint (= 1.0-1), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), bash-completion (= 1:2.16.0-8), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.2), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-1), gettext-base (= 1.0-1), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbrotli-dev (= 1.2.0-3), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl3t64-gnutls (= 8.21.0-2), libcurl4-gnutls (= 8.21.0-2), libcurl4-gnutls-dev (= 8.21.0-2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.2), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.12-stable-10+b2), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgnutls-dane0t64 (= 3.8.13-1), libgnutls28-dev (= 3.8.13-1), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhts-dev (= 1.22.1+ds2-1+b2), libhts3t64 (= 1.22.1+ds2-1+b2), libhtscodecs2 (= 1.6.6-1), libhwasan0 (= 16.1.0-2), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libio-pty-perl (= 1:1.31-1+b1), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.0-1), libk5crypto3 (= 1.22.1-3), libkadm5clnt-mit12 (= 1.22.1-3), libkadm5srv-mit12 (= 1.22.1-3), libkdb5-10t64 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5-dev (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap-dev (= 2.6.13+dfsg-1+b1), libldap2 (= 2.6.13+dfsg-1+b1), liblsan0 (= 16.1.0-2), liblzma-dev (= 5.8.3-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncurses-dev (= 6.6+20251231-1+b1), libncurses6 (= 6.6+20251231-1+b1), libncursesw6 (= 6.6+20251231-1+b1), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp2-dev (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libnghttp3-dev (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls-dev (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libngtcp2-dev (= 1.22.1-1), libp11-kit-dev (= 0.26.2-3), libp11-kit0 (= 0.26.2-3), libpam-modules (= 1.7.0-6), libpam-modules-bin (= 1.7.0-6), libpam-runtime (= 1.7.0-6), libpam0g (= 1.7.0-6), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc1-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.22.0-1), libpsl5t64 (= 0.22.0-1), libquadmath0 (= 16.1.0-2), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libssh2-1-dev (= 1.11.1-4), libssh2-1t64 (= 1.11.1-4), libssl-dev (= 3.6.3-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd0 (= 261.1-2), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20251231-1+b1), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunbound8 (= 1.25.1-1+b1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libzstd-dev (= 1.5.7+dfsg-3+b2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.0.13-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1+b1), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc1-1), perl-base (= 5.44.0~rc1-1), perl-modules-5.44 (= 5.44.0~rc1-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tabix (= 1.22.1+ds2-1+b2), tar (= 1.35+dfsg-4), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1755458966" +------------------------------------------------------------------------------+ | Package contents Mon, 29 Jun 2026 22:06:21 +0000 | +------------------------------------------------------------------------------+ samtools-dbgsym_1.22.1-1_amd64.deb ---------------------------------- new Debian package, version 2.0. size 1057300 bytes: control archive=900 bytes. 623 bytes, 12 lines control 827 bytes, 8 lines md5sums Package: samtools-dbgsym Source: samtools Version: 1.22.1-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1326 Depends: samtools (= 1.22.1-1) Section: debug Priority: optional Description: debug symbols for samtools Build-Ids: 012a06cec95aaad10bf8489fa4f1e057997d5431 26aab163c045d5a8e3481d0becdf6f2779ada204 5c696ec446ab91568f48396e7e66fa39c5ddf55c 9c8d5a88a699fa7871a7cd81017cd130230bd59d e071c9beb94795fb589405278723f925d8c73765 f8fbebab34efdd0b251496d87b983f628b01e768 ffd238be4a1087644896aee9c8eabafb518b870c drwxr-xr-x root/root 0 2025-08-17 19:29 ./ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/01/ -rw-r--r-- root/root 15960 2025-08-17 19:29 ./usr/lib/debug/.build-id/01/2a06cec95aaad10bf8489fa4f1e057997d5431.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/26/ -rw-r--r-- root/root 34264 2025-08-17 19:29 ./usr/lib/debug/.build-id/26/aab163c045d5a8e3481d0becdf6f2779ada204.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/5c/ -rw-r--r-- root/root 1209744 2025-08-17 19:29 ./usr/lib/debug/.build-id/5c/696ec446ab91568f48396e7e66fa39c5ddf55c.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/9c/ -rw-r--r-- root/root 15952 2025-08-17 19:29 ./usr/lib/debug/.build-id/9c/8d5a88a699fa7871a7cd81017cd130230bd59d.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/e0/ -rw-r--r-- root/root 15288 2025-08-17 19:29 ./usr/lib/debug/.build-id/e0/71c9beb94795fb589405278723f925d8c73765.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/f8/ -rw-r--r-- root/root 11360 2025-08-17 19:29 ./usr/lib/debug/.build-id/f8/fbebab34efdd0b251496d87b983f628b01e768.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.build-id/ff/ -rw-r--r-- root/root 28808 2025-08-17 19:29 ./usr/lib/debug/.build-id/ff/d238be4a1087644896aee9c8eabafb518b870c.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 4008 2025-08-17 19:29 ./usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-08-17 19:29 ./usr/share/doc/samtools-dbgsym -> samtools samtools-test_1.22.1-1_all.deb ------------------------------ new Debian package, version 2.0. size 2388504 bytes: control archive=16756 bytes. 518 bytes, 16 lines control 64749 bytes, 763 lines md5sums Package: samtools-test Source: samtools Version: 1.22.1-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 17236 Recommends: libio-pty-perl Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.htslib.org/ Description: test files for the samtools package Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. . This package contains test files for the samtools package. drwxr-xr-x root/root 0 2025-08-17 19:29 ./ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/doc/samtools-test/ -rw-r--r-- root/root 1278 2025-08-17 19:29 ./usr/share/doc/samtools-test/changelog.Debian.gz -rw-r--r-- root/root 41041 2025-07-14 11:11 ./usr/share/doc/samtools-test/changelog.gz -rw-r--r-- root/root 2250 2025-08-17 19:29 ./usr/share/doc/samtools-test/copyright drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/doc/samtools/ -rw-r--r-- root/root 364 2025-08-17 19:27 ./usr/share/doc/samtools/run-unit-test drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/ drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/ -rw-r--r-- root/root 1707 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/1_fixup.sam -rw-r--r-- root/root 1923 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/1_fixup.sam.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/1_fixup.sam.expected.err -rw-r--r-- root/root 1707 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam -rw-r--r-- root/root 1923 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected.err -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/3_fixup.sam.expected -rw-r--r-- root/root 79 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/3_fixup.sam.expected.err -rw-r--r-- root/root 1690 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam -rw-r--r-- root/root 1906 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected.err -rw-r--r-- root/root 1939 2025-07-14 11:11 ./usr/share/samtools/test/addrprg/5_editrg.sam.expected drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/ampliconclip/ -rw-r--r-- root/root 4288 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_delete_tag.expected.sam -rw-r--r-- root/root 4408 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_fail.expected.sam -rw-r--r-- root/root 1663 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_filter.expected.sam -rw-r--r-- root/root 3933 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_hard_clipped.expected.sam -rw-r--r-- root/root 4611 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_original_tag.expected.sam -rw-r--r-- root/root 4405 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_soft_clipped.expected.sam -rw-r--r-- root/root 178 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_soft_clipped_primer_counts.expected.tsv -rw-r--r-- root/root 4405 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_soft_clipped_strand.expected.sam -rw-r--r-- root/root 178 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_soft_clipped_strand_primer_counts.expected.tsv -rw-r--r-- root/root 4392 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/1_test_data.sam -rw-r--r-- root/root 2071 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/2_both_clipped.expected.sam -rw-r--r-- root/root 2075 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/2_both_test_data.sam -rw-r--r-- root/root 9276 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/3_multi_ref_both_clip.expected.sam -rw-r--r-- root/root 9270 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/3_multi_ref_clip.expected.sam -rw-r--r-- root/root 9229 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/3_multi_ref_data.sam -rw-r--r-- root/root 418 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/3_multi_ref_data_primer_counts.expected.tsv -rw-r--r-- root/root 572 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/4_total_hc_data.expected.sam -rw-r--r-- root/root 1016 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/4_total_hc_data.sam -rw-r--r-- root/root 145 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/ac_test.bed -rw-r--r-- root/root 12 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/ac_test2.bed -rw-r--r-- root/root 600 2025-07-14 11:11 ./usr/share/samtools/test/ampliconclip/multi_ref.bed drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/ampliconstats/ -rw-r--r-- root/root 9352 2025-07-14 11:11 ./usr/share/samtools/test/ampliconstats/mixed_clipped.sam -rw-r--r-- root/root 10637 2025-07-14 11:11 ./usr/share/samtools/test/ampliconstats/stats.expected.txt -rw-r--r-- root/root 5188 2025-07-14 11:11 ./usr/share/samtools/test/ampliconstats/stats_mixed.expected.txt -rw-r--r-- root/root 3708 2025-07-14 11:11 ./usr/share/samtools/test/ampliconstats/stats_partial.expected.txt drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/ -rw-r--r-- root/root 767 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/1.1.fq.expected -rw-r--r-- root/root 767 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/1.2.fq.expected -rw-r--r-- root/root 712 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/10.1.fq.expected -rw-r--r-- root/root 712 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/10.2.fq.expected -rw-r--r-- root/root 96 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/10.s.fq.expected -rw-r--r-- root/root 1098 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/11.fa.expected -rw-r--r-- root/root 1606 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/11.fq.expected -rw-r--r-- root/root 864 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/12.1.fq.expected -rw-r--r-- root/root 864 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/12.2.fq.expected -rw-r--r-- root/root 116 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/12.i.fq.expected -rw-r--r-- root/root 112 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/12.s.fq.expected -rw-r--r-- root/root 219 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/13.fq.expected -rw-r--r-- root/root 53 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/14.0.fq.expected -rw-r--r-- root/root 25 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/14.i1.fq.expected -rw-r--r-- root/root 25 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/14.i2.fq.expected -rw-r--r-- root/root 3094 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/15.fq.expected -rw-r--r-- root/root 2280 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/16.fq.expected -rw-r--r-- root/root 2647 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/17.fq.expected -rw-r--r-- root/root 474 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/18.fq.expected -rw-r--r-- root/root 250 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/19.fq.expected -rw-r--r-- root/root 767 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/2.1.fq.expected -rw-r--r-- root/root 767 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/2.2.fq.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/2.s.fq.expected -rw-r--r-- root/root 156 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/20.fq.expected -rw-r--r-- root/root 767 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/3.1.fq.expected -rw-r--r-- root/root 767 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/3.2.fq.expected -rw-r--r-- root/root 41 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/3.s.fq.expected -rw-r--r-- root/root 712 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/4.1.fq.expected -rw-r--r-- root/root 712 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/4.2.fq.expected -rw-r--r-- root/root 96 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/4.s.fq.expected -rw-r--r-- root/root 746 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/5.1.fq.expected -rw-r--r-- root/root 746 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/5.2.fq.expected -rw-r--r-- root/root 100 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/5.s.fq.expected -rw-r--r-- root/root 964 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/6.1.fq.expected -rw-r--r-- root/root 916 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/6.2.fq.expected -rw-r--r-- root/root 120 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/6.s.fq.expected -rw-r--r-- root/root 1198 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/7.1.fq.expected -rw-r--r-- root/root 1104 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/7.2.fq.expected -rw-r--r-- root/root 128 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/7.s.fq.expected -rw-r--r-- root/root 861 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/8.1.fq.expected -rw-r--r-- root/root 861 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/8.2.fq.expected -rw-r--r-- root/root 109 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/8.i.fq.expected -rw-r--r-- root/root 112 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/8.s.fq.expected -rw-r--r-- root/root 1669 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/9.1.fq.expected -rw-r--r-- root/root 717 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/9.2.fq.expected -rw-r--r-- root/root 72 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/bc.fq.expected -rw-r--r-- root/root 72 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/bc10.fq.expected -rw-r--r-- root/root 82 2025-07-14 11:11 ./usr/share/samtools/test/bam2fq/bc_split.fq.expected drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/ -rw-r--r-- root/root 6152 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov.bam -rw-r--r-- root/root 7608 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov.bam.bai -rw-r--r-- root/root 23 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov.bed -rw-r--r-- root/root 26 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov.expected -rw-r--r-- root/root 31 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov_c.expected -rw-r--r-- root/root 23 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov_gG.bed -rw-r--r-- root/root 28 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov_gG.expected -rw-r--r-- root/root 25 2025-07-14 11:11 ./usr/share/samtools/test/bedcov/bedcov_j.expected drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/checksum/ -rw-r--r-- root/root 497 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk1.1.expected -rw-r--r-- root/root 1366 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk1.3.expected -rw-r--r-- root/root 9877 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk1.bam -rw-r--r-- root/root 497 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk2.1.expected -rw-r--r-- root/root 720 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk2.2.expected -rw-r--r-- root/root 1129 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk2.3.expected -rw-r--r-- root/root 1592 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk2.4.expected -rw-r--r-- root/root 6879 2025-07-14 11:11 ./usr/share/samtools/test/checksum/chk2.cram drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/collate/ -rw-r--r-- root/root 12246 2025-07-14 11:11 ./usr/share/samtools/test/collate/1_fast_collate.sam.expected -rw-r--r-- root/root 12246 2025-07-14 11:11 ./usr/share/samtools/test/collate/2_fast_collate_with_tmp_used.sam.expected -rw-r--r-- root/root 1440 2025-07-14 11:11 ./usr/share/samtools/test/collate/collate.expected.sam -rw-r--r-- root/root 14085 2025-07-14 11:11 ./usr/share/samtools/test/collate/fast_collate.sam drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/consensus/ -rw-r--r-- root/root 524 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consen1.sam -rw-r--r-- root/root 490 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consen1b.sam -rw-r--r-- root/root 86 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consen1c.fa -rw-r--r-- root/root 59 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consen1c.fa.fai -rw-r--r-- root/root 627 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consen1c.sam -rw-r--r-- root/root 147 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consen2.sam -rw-r--r-- root/root 750 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consen3.sam -rw-r--r-- root/root 9996 2025-07-14 11:11 ./usr/share/samtools/test/consensus/consensus.reg drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/ -rw-r--r-- root/root 21 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/1.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/10.1q.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/10q.out -rw-r--r-- root/root 453 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/11.3p.out -rw-r--r-- root/root 42 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/11.3q.out -rw-r--r-- root/root 429 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/11.6p.out -rw-r--r-- root/root 42 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/11.6q.out -rw-r--r-- root/root 312 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/12p.out -rw-r--r-- root/root 56 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/12q.out -rw-r--r-- root/root 644 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/13p.out -rw-r--r-- root/root 86 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/13q.out -rw-r--r-- root/root 34 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/14p.out -rw-r--r-- root/root 12 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/14q.out -rw-r--r-- root/root 36 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/15p.out -rw-r--r-- root/root 220 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/16p.out -rw-r--r-- root/root 32 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/16q.out -rw-r--r-- root/root 94 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/17q.out -rw-r--r-- root/root 412 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/18p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/18q.out -rw-r--r-- root/root 411 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/19p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/19q.out -rw-r--r-- root/root 426 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/1p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/1q.out -rw-r--r-- root/root 22 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/2.out -rw-r--r-- root/root 417 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/20p.out -rw-r--r-- root/root 417 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/21p.out -rw-r--r-- root/root 426 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/22p.out -rw-r--r-- root/root 387 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/23p.out -rw-r--r-- root/root 370 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/24p.out -rw-r--r-- root/root 426 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/25p.out -rw-r--r-- root/root 426 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/26p.out -rw-r--r-- root/root 412 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/2p.out -rw-r--r-- root/root 42 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/2q.out -rw-r--r-- root/root 15 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/3.out -rw-r--r-- root/root 90 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/30.out -rw-r--r-- root/root 90 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/30T.out -rw-r--r-- root/root 108 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/31.out -rw-r--r-- root/root 108 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/31T.out -rw-r--r-- root/root 164 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/32.out -rw-r--r-- root/root 164 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/32T.out -rw-r--r-- root/root 28 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/3q.out -rw-r--r-- root/root 16 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/4.out -rw-r--r-- root/root 633 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/40.out -rw-r--r-- root/root 633 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/40T.out -rw-r--r-- root/root 898 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/41.out -rw-r--r-- root/root 898 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/41T.out -rw-r--r-- root/root 1240 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/42.out -rw-r--r-- root/root 1240 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/42T.out -rw-r--r-- root/root 412 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/4p.out -rw-r--r-- root/root 30 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/4q.out -rw-r--r-- root/root 419 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/5p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/5q.out -rw-r--r-- root/root 432 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/6p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/6q.out -rw-r--r-- root/root 432 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/7p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/7q.out -rw-r--r-- root/root 433 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/8p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/8q.out -rw-r--r-- root/root 419 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/9.1p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/9.1q.out -rw-r--r-- root/root 420 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/9p.out -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/9q.out -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/consensus/expected/empty.out drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/cram_size/ -rw-r--r-- root/root 439 2025-07-14 11:11 ./usr/share/samtools/test/cram_size/cram_size.reg drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/cram_size/expected/ -rw-r--r-- root/root 4973 2025-07-14 11:11 ./usr/share/samtools/test/cram_size/expected/encodings.out -rw-r--r-- root/root 2133 2025-07-14 11:11 ./usr/share/samtools/test/cram_size/expected/normal.out -rw-r--r-- root/root 3150 2025-07-14 11:11 ./usr/share/samtools/test/cram_size/expected/verbose.out -rw-r--r-- root/root 60965 2025-07-14 11:11 ./usr/share/samtools/test/cram_size/mpileup.1.cram drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/dat/ -rw-r--r-- root/root 5471 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.001.sam -rw-r--r-- root/root 5573 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.002.sam -rw-r--r-- root/root 5493 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.003.sam -rw-r--r-- root/root 5503 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.004.sam -rw-r--r-- root/root 5508 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.005.sam -rw-r--r-- root/root 5535 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.010.sam -rw-r--r-- root/root 1594 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.013.sam -rw-r--r-- root/root 112 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.014.sam -rw-r--r-- root/root 9707 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.703.sam -rw-r--r-- root/root 37 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.MD-D -rw-r--r-- root/root 6 2025-07-14 11:11 ./usr/share/samtools/test/dat/bam2fq.NM-D -rw-r--r-- root/root 1292 2025-07-14 11:11 ./usr/share/samtools/test/dat/cat.hdr drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/dat/cram_md5/ -rw-r--r-- root/root 57 2025-07-14 11:11 ./usr/share/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 -rw-r--r-- root/root 61 2025-07-14 11:11 ./usr/share/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 -rw-r--r-- root/root 36 2025-07-14 11:11 ./usr/share/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 -rw-r--r-- root/root 31 2025-07-14 11:11 ./usr/share/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b -rw-r--r-- root/root 42 2025-07-14 11:11 ./usr/share/samtools/test/dat/depad.001.fa -rw-r--r-- root/root 16 2025-07-14 11:11 ./usr/share/samtools/test/dat/depad.001.fa.fai -rw-r--r-- root/root 7964 2025-07-14 11:11 ./usr/share/samtools/test/dat/depad.001p.sam -rw-r--r-- root/root 7998 2025-07-14 11:11 ./usr/share/samtools/test/dat/depad.001u.sam -rw-r--r-- root/root 135 2025-07-14 11:11 ./usr/share/samtools/test/dat/dict.alias.fa -rw-r--r-- root/root 618 2025-07-14 11:11 ./usr/share/samtools/test/dat/dict.alias.out -rw-r--r-- root/root 46 2025-07-14 11:11 ./usr/share/samtools/test/dat/dict.alt -rw-r--r-- root/root 525 2025-07-14 11:11 ./usr/share/samtools/test/dat/dict.alt.out -rw-r--r-- root/root 2300 2025-07-14 11:11 ./usr/share/samtools/test/dat/dict.fa -rw-r--r-- root/root 1484 2025-07-14 11:11 ./usr/share/samtools/test/dat/dict.out -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/dat/empty.expected -rw-r--r-- root/root 624 2025-07-14 11:11 ./usr/share/samtools/test/dat/large_chrom.out -rw-r--r-- root/root 5090 2025-07-14 11:11 ./usr/share/samtools/test/dat/large_chrom.sam -rw-r--r-- root/root 92 2025-07-14 11:11 ./usr/share/samtools/test/dat/large_chrom_bai_index.err -rw-r--r-- root/root 350835 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.1.sam -rw-r--r-- root/root 104818 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.2.sam -rw-r--r-- root/root 105780 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.3.sam -rw-r--r-- root/root 37 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.err.1 -rw-r--r-- root/root 2715 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.out.1 -rw-r--r-- root/root 81714 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.out.2 -rw-r--r-- root/root 295 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.out.3 -rw-r--r-- root/root 113952 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.out.4 -rw-r--r-- root/root 23 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.out.5 -rw-r--r-- root/root 4284 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.ref.fa -rw-r--r-- root/root 17 2025-07-14 11:11 ./usr/share/samtools/test/dat/mpileup.ref.fa.fai -rw-r--r-- root/root 74 2025-07-14 11:11 ./usr/share/samtools/test/dat/nested.bed -rw-r--r-- root/root 1965 2025-07-14 11:11 ./usr/share/samtools/test/dat/nested.expected.sam -rw-r--r-- root/root 819 2025-07-14 11:11 ./usr/share/samtools/test/dat/sort_name_input_1.sam -rw-r--r-- root/root 759 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_a.bam -rw-r--r-- root/root 264 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_a.bam.bai.expected -rw-r--r-- root/root 3178 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_a.cram -rw-r--r-- root/root 1429 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_a.sam -rw-r--r-- root/root 1576 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_a_regex.sam -rw-r--r-- root/root 1349 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_ab.X.expected -rw-r--r-- root/root 545 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_b.X.expected -rw-r--r-- root/root 1014 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_b.X2.expected -rw-r--r-- root/root 686 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_b.bam -rw-r--r-- root/root 1252 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_b.sam -rw-r--r-- root/root 1369 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_b_regex.sam -rw-r--r-- root/root 692 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_c.bam -rw-r--r-- root/root 1293 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_c.sam -rw-r--r-- root/root 1419 2025-07-14 11:11 ./usr/share/samtools/test/dat/test_input_1_d.sam -rw-r--r-- root/root 1335 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.001.01.bed -rw-r--r-- root/root 1134 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.001.02.bed -rw-r--r-- root/root 1349 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.001.03.bed -rw-r--r-- root/root 214 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.001.fa -rw-r--r-- root/root 58 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.001.fa.fai -rw-r--r-- root/root 5121 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.001.sam -rw-r--r-- root/root 1313 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.002.01.bed -rw-r--r-- root/root 1302 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.002.02.bed -rw-r--r-- root/root 64 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.002.fa -rw-r--r-- root/root 13 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.002.fa.fai -rw-r--r-- root/root 3692 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.002.sam -rw-r--r-- root/root 2142 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.003.expected.sam -rw-r--r-- root/root 2224 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.003.sam -rw-r--r-- root/root 5158 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.004.expected.sam -rw-r--r-- root/root 4052 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.005.expected.sam -rw-r--r-- root/root 4392 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.005.sam -rw-r--r-- root/root 4322 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.005.unmap.expected.sam -rw-r--r-- root/root 7319 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.fetch-pairs.bam -rw-r--r-- root/root 16156 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.fetch-pairs.expected.sam -rw-r--r-- root/root 19190 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.fetch-pairs.filter0.expected.sam -rw-r--r-- root/root 16153 2025-07-14 11:11 ./usr/share/samtools/test/dat/view.fetch-pairs.filter1.expected.sam drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/ -rw-r--r-- root/root 965 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/1_coord_sort.sam -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected -rw-r--r-- root/root 82 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected.err -rw-r--r-- root/root 1118 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam -rw-r--r-- root/root 1260 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam.expected -rw-r--r-- root/root 715 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam -rw-r--r-- root/root 733 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected -rw-r--r-- root/root 715 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam -rw-r--r-- root/root 733 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected -rw-r--r-- root/root 715 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/5_ct.sam -rw-r--r-- root/root 753 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/5_ct.sam.expected -rw-r--r-- root/root 735 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/6_ct_replace.sam -rw-r--r-- root/root 753 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/6_ct_replace.sam.expected -rw-r--r-- root/root 1191 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/7_two_read_mapped.sam -rw-r--r-- root/root 1334 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/7_two_read_mapped.sam.expected -rw-r--r-- root/root 1327 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/8_isize_overflow_64bit.sam -rw-r--r-- root/root 1508 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/8_isize_overflow_64bit.sam.expected -rw-r--r-- root/root 436 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ML_only.sam -rw-r--r-- root/root 369 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ML_only.sam.expected -rw-r--r-- root/root 458 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ML_wrong_len.sam -rw-r--r-- root/root 360 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ML_wrong_len.sam.expected -rw-r--r-- root/root 400 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_MN_only.sam -rw-r--r-- root/root 369 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_MN_only.sam.expected -rw-r--r-- root/root 561 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_bad_MN.sam -rw-r--r-- root/root 561 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_bad_MN.sam.expected -rw-r--r-- root/root 280 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_bounds.sam -rw-r--r-- root/root 244 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_bounds.sam.expected -rw-r--r-- root/root 549 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_draft.sam -rw-r--r-- root/root 549 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_draft.sam.expected -rw-r--r-- root/root 441 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_noseq.sam -rw-r--r-- root/root 369 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_noseq.sam.expected -rw-r--r-- root/root 1042 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_not_updated.sam -rw-r--r-- root/root 922 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_not_updated.sam.expected -rw-r--r-- root/root 866 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_not_updated_noML.sam -rw-r--r-- root/root 815 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_not_updated_noML.sam.expected -rw-r--r-- root/root 978 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_not_updated_noMN.sam -rw-r--r-- root/root 922 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_not_updated_noMN.sam.expected -rw-r--r-- root/root 890 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_not_updated_noseq.sam -rw-r--r-- root/root 549 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ok+.sam -rw-r--r-- root/root 549 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ok+.sam.expected -rw-r--r-- root/root 550 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ok-.sam -rw-r--r-- root/root 550 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/mod_ok-.sam.expected -rw-r--r-- root/root 2884 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/sanitize.sam -rw-r--r-- root/root 2818 2025-07-14 11:11 ./usr/share/samtools/test/fixmate/sanitize.sam.expected drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/idxstats/ -rw-r--r-- root/root 58 2025-07-14 11:11 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected.err drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/import/ -rw-r--r-- root/root 2518 2025-07-14 11:11 ./usr/share/samtools/test/import/1.expected.sam -rw-r--r-- root/root 1705 2025-07-14 11:11 ./usr/share/samtools/test/import/2.expected.sam -rw-r--r-- root/root 1320 2025-07-14 11:11 ./usr/share/samtools/test/import/2.interleaved.fq -rw-r--r-- root/root 1344 2025-07-14 11:11 ./usr/share/samtools/test/import/3.interleaved.fq -rw-r--r-- root/root 286 2025-07-14 11:11 ./usr/share/samtools/test/import/4.aux.fq -rw-r--r-- root/root 342 2025-07-14 11:11 ./usr/share/samtools/test/import/4.expected-XZ,XA,AA.sam -rw-r--r-- root/root 414 2025-07-14 11:11 ./usr/share/samtools/test/import/4.expected.sam -rw-r--r-- root/root 382 2025-07-14 11:11 ./usr/share/samtools/test/import/5-BC.expected.sam -rw-r--r-- root/root 382 2025-07-14 11:11 ./usr/share/samtools/test/import/5-OX.expected.sam -rw-r--r-- root/root 26 2025-07-14 11:11 ./usr/share/samtools/test/import/5-i1.fq -rw-r--r-- root/root 34 2025-07-14 11:11 ./usr/share/samtools/test/import/5-i2.fq -rw-r--r-- root/root 66 2025-07-14 11:11 ./usr/share/samtools/test/import/5-r1.fq -rw-r--r-- root/root 66 2025-07-14 11:11 ./usr/share/samtools/test/import/5-r2.fq drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/ -rw-r--r-- root/root 6292 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/depth.expected.out -rw-r--r-- root/root 82 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/depth_bed.expected.out -rw-r--r-- root/root 31742 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/longref.sam -rw-r--r-- root/root 28433 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/longref2.sam -rw-r--r-- root/root 4740 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/longref3.expected.sam -rw-r--r-- root/root 2947 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/longref3.sam -rw-r--r-- root/root 6721 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/longref_idx.expected.sam -rw-r--r-- root/root 31741 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/longref_name.sam -rw-r--r-- root/root 60115 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/merge.expected.sam -rw-r--r-- root/root 37 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/test.bed -rw-r--r-- root/root 3888 2025-07-14 11:11 ./usr/share/samtools/test/large_pos/tview.expected.out drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/maintainer/ -rwxr-xr-x root/root 3237 2025-07-14 11:11 ./usr/share/samtools/test/maintainer/check_copyright.pl -rwxr-xr-x root/root 2928 2025-07-14 11:11 ./usr/share/samtools/test/maintainer/check_spaces.pl drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/markdup/ -rw-r--r-- root/root 2068 2025-07-14 11:11 ./usr/share/samtools/test/markdup/10_optical_chain.expected.sam -rw-r--r-- root/root 1850 2025-07-14 11:11 ./usr/share/samtools/test/markdup/10_optical_chain.sam -rw-r--r-- root/root 4392 2025-07-14 11:11 ./usr/share/samtools/test/markdup/11_optical_dup_regex.expected.sam -rw-r--r-- root/root 4052 2025-07-14 11:11 ./usr/share/samtools/test/markdup/11_optical_dup_regex.sam -rw-r--r-- root/root 2777 2025-07-14 11:11 ./usr/share/samtools/test/markdup/12_optical_chain_regex.expected.sam -rw-r--r-- root/root 2450 2025-07-14 11:11 ./usr/share/samtools/test/markdup/12_optical_chain_regex.sam -rw-r--r-- root/root 3292 2025-07-14 11:11 ./usr/share/samtools/test/markdup/13_optical_barcode_tag.expected.sam -rw-r--r-- root/root 2782 2025-07-14 11:11 ./usr/share/samtools/test/markdup/13_optical_barcode_tag.sam -rw-r--r-- root/root 3883 2025-07-14 11:11 ./usr/share/samtools/test/markdup/14_optical_barcode_name.expected.sam -rw-r--r-- root/root 2908 2025-07-14 11:11 ./usr/share/samtools/test/markdup/14_optical_barcode_name.sam -rw-r--r-- root/root 3784 2025-07-14 11:11 ./usr/share/samtools/test/markdup/15_optical_barcode_rgx_name.expected.sam -rw-r--r-- root/root 2854 2025-07-14 11:11 ./usr/share/samtools/test/markdup/15_optical_barcode_rgx_name.sam -rw-r--r-- root/root 3751 2025-07-14 11:11 ./usr/share/samtools/test/markdup/16_optical_barcode_rgx_name_test_2.expected.sam -rw-r--r-- root/root 2836 2025-07-14 11:11 ./usr/share/samtools/test/markdup/16_optical_barcode_rgx_name_test_2.sam -rw-r--r-- root/root 3118 2025-07-14 11:11 ./usr/share/samtools/test/markdup/17_read_group.expected.sam -rw-r--r-- root/root 2608 2025-07-14 11:11 ./usr/share/samtools/test/markdup/17_read_group.sam -rw-r--r-- root/root 25862 2025-07-14 11:11 ./usr/share/samtools/test/markdup/18_primary_duplicate_count.expected.sam -rw-r--r-- root/root 25282 2025-07-14 11:11 ./usr/share/samtools/test/markdup/18_primary_duplicate_count.sam -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/markdup/1_name_sort.expected.sam -rw-r--r-- root/root 65 2025-07-14 11:11 ./usr/share/samtools/test/markdup/1_name_sort.expected.sam.err -rw-r--r-- root/root 9635 2025-07-14 11:11 ./usr/share/samtools/test/markdup/1_name_sort.sam -rw-r--r-- root/root 3076 2025-07-14 11:11 ./usr/share/samtools/test/markdup/2_bad_order.expected.sam -rw-r--r-- root/root 39 2025-07-14 11:11 ./usr/share/samtools/test/markdup/2_bad_order.expected.sam.err -rw-r--r-- root/root 10226 2025-07-14 11:11 ./usr/share/samtools/test/markdup/2_bad_order.sam -rw-r--r-- root/root 58 2025-07-14 11:11 ./usr/share/samtools/test/markdup/3_missing_mc.expected.sam -rw-r--r-- root/root 77 2025-07-14 11:11 ./usr/share/samtools/test/markdup/3_missing_mc.expected.sam.err -rw-r--r-- root/root 9626 2025-07-14 11:11 ./usr/share/samtools/test/markdup/3_missing_mc.sam -rw-r--r-- root/root 58 2025-07-14 11:11 ./usr/share/samtools/test/markdup/4_missing_ms.expected.sam -rw-r--r-- root/root 68 2025-07-14 11:11 ./usr/share/samtools/test/markdup/4_missing_ms.expected.sam.err -rw-r--r-- root/root 9626 2025-07-14 11:11 ./usr/share/samtools/test/markdup/4_missing_ms.sam -rw-r--r-- root/root 9644 2025-07-14 11:11 ./usr/share/samtools/test/markdup/5_markdup.expected.sam -rw-r--r-- root/root 9636 2025-07-14 11:11 ./usr/share/samtools/test/markdup/5_markdup.sam -rw-r--r-- root/root 6038 2025-07-14 11:11 ./usr/share/samtools/test/markdup/6_remove_dups.expected.sam -rw-r--r-- root/root 9636 2025-07-14 11:11 ./usr/share/samtools/test/markdup/6_remove_dups.sam -rw-r--r-- root/root 13220 2025-07-14 11:11 ./usr/share/samtools/test/markdup/7_mark_supp_dup.expected.sam -rw-r--r-- root/root 13206 2025-07-14 11:11 ./usr/share/samtools/test/markdup/7_mark_supp_dup.sam -rw-r--r-- root/root 4392 2025-07-14 11:11 ./usr/share/samtools/test/markdup/8_optical_dup.expected.sam -rw-r--r-- root/root 4052 2025-07-14 11:11 ./usr/share/samtools/test/markdup/8_optical_dup.sam -rw-r--r-- root/root 2606 2025-07-14 11:11 ./usr/share/samtools/test/markdup/9_optical_dup_qcfail.expected.sam -rw-r--r-- root/root 2433 2025-07-14 11:11 ./usr/share/samtools/test/markdup/9_optical_dup_qcfail.sam drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/merge/ -rw-r--r-- root/root 4133 2025-07-14 11:11 ./usr/share/samtools/test/merge/2.merge.expected.sam -rw-r--r-- root/root 174 2025-07-14 11:11 ./usr/share/samtools/test/merge/3.merge.expected.err -rw-r--r-- root/root 4097 2025-07-14 11:11 ./usr/share/samtools/test/merge/3.merge.expected.sam -rw-r--r-- root/root 1252 2025-07-14 11:11 ./usr/share/samtools/test/merge/4.merge.expected.sam -rw-r--r-- root/root 4153 2025-07-14 11:11 ./usr/share/samtools/test/merge/5.merge.expected.sam -rw-r--r-- root/root 2423 2025-07-14 11:11 ./usr/share/samtools/test/merge/6.merge.expected.sam -rw-r--r-- root/root 2875 2025-07-14 11:11 ./usr/share/samtools/test/merge/7.merge.expected.sam -rw-r--r-- root/root 40 2025-07-14 11:11 ./usr/share/samtools/test/merge/merge.bed -rw-r--r-- root/root 575 2025-07-14 11:11 ./usr/share/samtools/test/merge/merge.bed.1.sam -rw-r--r-- root/root 211 2025-07-14 11:11 ./usr/share/samtools/test/merge/merge.bed.2.sam -rw-r--r-- root/root 340 2025-07-14 11:11 ./usr/share/samtools/test/merge/merge.bed.expected.sam -rw-r--r-- root/root 1386 2025-07-14 11:11 ./usr/share/samtools/test/merge/rg_from_r_mode.expected.sam -rw-r--r-- root/root 2461 2025-07-14 11:11 ./usr/share/samtools/test/merge/tag.pg.merge.expected.sam -rw-r--r-- root/root 2553 2025-07-14 11:11 ./usr/share/samtools/test/merge/tag.pg.n.merge.expected.sam -rw-r--r-- root/root 46 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_3.fofn -rw-r--r-- root/root 15964 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_bam_translate.c -rw-r--r-- root/root 184 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_header.sam -rw-r--r-- root/root 1032 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_no_pg_rg_co.sam -rw-r--r-- root/root 3556 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_rtrans_build.c -rw-r--r-- root/root 3035 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_template_coordinate.1.sam -rw-r--r-- root/root 3046 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_template_coordinate.2.sam -rw-r--r-- root/root 5956 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_template_coordinate.expected.sam -rw-r--r-- root/root 17007 2025-07-14 11:11 ./usr/share/samtools/test/merge/test_trans_tbl_init.c drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/mpileup/ -rw-r--r-- root/root 525 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/1read.bam -rw-r--r-- root/root 5 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/1read.sam -rw-r--r-- root/root 1886 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/anomalous.sam -rw-r--r-- root/root 265 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/c1#clip.bam -rw-r--r-- root/root 299 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/c1#pad1.bam -rw-r--r-- root/root 349 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/c1#pad2.bam -rw-r--r-- root/root 382 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/c1#pad3.bam -rw-r--r-- root/root 29 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/c1.fa -rw-r--r-- root/root 557 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#5b.bam -rw-r--r-- root/root 416 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#5b.bam.bai -rw-r--r-- root/root 13183 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#5b.cram -rw-r--r-- root/root 75 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#5b.cram.crai -rw-r--r-- root/root 2033 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#5b.sam -rw-r--r-- root/root 345315 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#large_seq.bam -rw-r--r-- root/root 233 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#unmap.bam -rw-r--r-- root/root 896 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#unmap1.bam -rw-r--r-- root/root 1344 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce#unmap2.bam -rw-r--r-- root/root 1060702 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/ce.fa -rw-r--r-- root/root 1568 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/cram-size.reg -rw-r--r-- root/root 252022 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/deep.sam -rw-r--r-- root/root 5840 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/depth.reg -rw-r--r-- root/root 116 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/depth_del.sam drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/mpileup/expected/ -rw-r--r-- root/root 596103 2025-08-17 19:29 ./usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz -rw-r--r-- root/root 607 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/10.out -rw-r--r-- root/root 238 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/11.out -rw-r--r-- root/root 330 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/12.out -rw-r--r-- root/root 163523 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/13.out -rw-r--r-- root/root 282190 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/14.out -rw-r--r-- root/root 282190 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/15.out -rw-r--r-- root/root 162736 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/16.out -rw-r--r-- root/root 163523 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/17.out -rw-r--r-- root/root 163523 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/18.out -rw-r--r-- root/root 162736 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/19.out -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/2.out -rw-r--r-- root/root 64851 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/20.out -rw-r--r-- root/root 162736 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/21.out -rw-r--r-- root/root 162736 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/22.out -rw-r--r-- root/root 2254 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/23.out -rw-r--r-- root/root 2354 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/24.out -rw-r--r-- root/root 2354 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/25.out -rw-r--r-- root/root 1706 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/26.out -rw-r--r-- root/root 2112 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/27.out -rw-r--r-- root/root 165459 2025-07-14 11:11 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2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/39.out -rw-r--r-- root/root 4352 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/4.out -rw-r--r-- root/root 2155 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/40.out -rw-r--r-- root/root 559 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/41.out -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/42.out -rw-r--r-- root/root 103148 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/43.out -rw-r--r-- root/root 103148 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/44.out -rw-r--r-- root/root 111941 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/45.out -rw-r--r-- root/root 111941 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/46.out -rw-r--r-- root/root 5 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/47.out -rw-r--r-- root/root 383633 2025-07-14 11:11 ./usr/share/samtools/test/mpileup/expected/48.out 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./usr/share/samtools/test/quickcheck/6.quickcheck.cram21.ok.cram -rw-r--r-- root/root 49122 2025-07-14 11:11 ./usr/share/samtools/test/quickcheck/7.quickcheck.cram30.ok.cram -rw-r--r-- root/root 154413 2025-07-14 11:11 ./usr/share/samtools/test/quickcheck/8.quickcheck.cram21.truncated.cram -rw-r--r-- root/root 49084 2025-07-14 11:11 ./usr/share/samtools/test/quickcheck/9.quickcheck.cram30.truncated.cram -rw-r--r-- root/root 188 2025-07-14 11:11 ./usr/share/samtools/test/quickcheck/all.expected drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/reference/ -rw-r--r-- root/root 4274 2025-07-14 11:11 ./usr/share/samtools/test/reference/mpileup.MD.fa.expected -rw-r--r-- root/root 4274 2025-07-14 11:11 ./usr/share/samtools/test/reference/mpileup.embed.fa.expected -rwxr-xr-x root/root 4969 2025-07-14 11:11 ./usr/share/samtools/test/regression.sh drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/reheader/ -rw-r--r-- root/root 5079 2025-07-14 11:11 ./usr/share/samtools/test/reheader/1_view1.sam.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/reheader/1_view1.sam.expected.err -rw-r--r-- root/root 5079 2025-07-14 11:11 ./usr/share/samtools/test/reheader/2_view1.sam.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/reheader/2_view1.sam.expected.err -rw-r--r-- root/root 5079 2025-07-14 11:11 ./usr/share/samtools/test/reheader/3_view1.sam.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/reheader/3_view1.sam.expected.err -rw-r--r-- root/root 5127 2025-07-14 11:11 ./usr/share/samtools/test/reheader/4_view1.sam.expected -rw-r--r-- root/root 5121 2025-07-14 11:11 ./usr/share/samtools/test/reheader/5_view1.sam.expected -rw-r--r-- root/root 1477 2025-07-14 11:11 ./usr/share/samtools/test/reheader/hdr.sam drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/reset/ -rw-r--r-- root/root 227042 2025-07-14 11:11 ./usr/share/samtools/test/reset/basic.1.mp.1.expected -rw-r--r-- root/root 1128 2025-07-14 11:11 ./usr/share/samtools/test/reset/basic.bam.input.expected -rw-r--r-- root/root 1128 2025-07-14 11:11 ./usr/share/samtools/test/reset/basic.cram.input.expected -rw-r--r-- root/root 231141 2025-07-14 11:11 ./usr/share/samtools/test/reset/basic.output.mp.1.expected -rw-r--r-- root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/reset/empty.expected -rw-r--r-- root/root 164 2025-07-14 11:11 ./usr/share/samtools/test/reset/output.flg.1.expected -rw-r--r-- root/root 162 2025-07-14 11:11 ./usr/share/samtools/test/reset/output.flg.2.expected -rw-r--r-- root/root 146152 2025-07-14 11:11 ./usr/share/samtools/test/reset/output.keep.1.expected -rw-r--r-- root/root 210821 2025-07-14 11:11 ./usr/share/samtools/test/reset/output.keep.2.expected -rw-r--r-- root/root 149995 2025-07-14 11:11 ./usr/share/samtools/test/reset/output.keep.3.expected -rw-r--r-- root/root 218507 2025-07-14 11:11 ./usr/share/samtools/test/reset/output.nRG.1.expected -rw-r--r-- root/root 136575 2025-07-14 11:11 ./usr/share/samtools/test/reset/output.nRG.2.expected -rw-r--r-- root/root 2 2025-07-14 11:11 ./usr/share/samtools/test/reset/reject.1.expected -rw-r--r-- root/root 3 2025-07-14 11:11 ./usr/share/samtools/test/reset/reject.2.expected -rw-r--r-- root/root 382 2025-07-14 11:11 ./usr/share/samtools/test/reset/seq.sam drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/sort/ -rw-r--r-- root/root 336994 2025-07-14 11:11 ./usr/share/samtools/test/sort/minimiser-basic.sam -rw-r--r-- root/root 358929 2025-07-14 11:11 ./usr/share/samtools/test/sort/minimiser-indexed-poly.sam -rw-r--r-- root/root 358890 2025-07-14 11:11 ./usr/share/samtools/test/sort/minimiser-indexed.sam -rw-r--r-- root/root 1463 2025-07-14 11:11 ./usr/share/samtools/test/sort/name.sort.expected.sam -rw-r--r-- root/root 1294 2025-07-14 11:11 ./usr/share/samtools/test/sort/name2.sort.expected.sam -rw-r--r-- root/root 944 2025-07-14 11:11 ./usr/share/samtools/test/sort/name3.sort.expected.sam -rw-r--r-- root/root 1443 2025-07-14 11:11 ./usr/share/samtools/test/sort/pos.sort.expected.sam -rw-r--r-- root/root 1430 2025-07-14 11:11 ./usr/share/samtools/test/sort/tag.as.sort.expected.sam -rw-r--r-- root/root 1430 2025-07-14 11:11 ./usr/share/samtools/test/sort/tag.fi.sort.expected.sam -rw-r--r-- root/root 1440 2025-07-14 11:11 ./usr/share/samtools/test/sort/tag.rg.n.sort.expected.sam -rw-r--r-- root/root 1440 2025-07-14 11:11 ./usr/share/samtools/test/sort/tag.rg.sort.expected.sam -rw-r--r-- root/root 3185 2025-07-14 11:11 ./usr/share/samtools/test/sort/template-coordinate.sort.expected.sam -rw-r--r-- root/root 3144 2025-07-14 11:11 ./usr/share/samtools/test/sort/template-coordinate.sort.sam drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/split/ -rw-r--r-- root/root 3169 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected.grp1.sam -rw-r--r-- root/root 2924 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected.grp2.sam -rw-r--r-- root/root 2085 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected.unk.sam -rw-r--r-- root/root 1628 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_RG.grp3.sam -rw-r--r-- root/root 1869 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_RG.unk.sam -rw-r--r-- root/root 1930 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_an.aardvark.sam -rw-r--r-- root/root 2870 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_an.badger.sam -rw-r--r-- root/root 2595 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_an.cat.sam -rw-r--r-- root/root 2076 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_an.dog.sam -rw-r--r-- root/root 1865 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_an.unk.sam -rw-r--r-- root/root 2303 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_an_M_3.unk.sam -rw-r--r-- root/root 1937 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_nn.-1.sam -rw-r--r-- root/root 2317 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_nn.-2.sam -rw-r--r-- root/root 2064 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_nn.1.sam -rw-r--r-- root/root 3153 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_nn.2.sam -rw-r--r-- root/root 2072 2025-07-14 11:11 ./usr/share/samtools/test/split/split.expected_d_nn.unk.sam -rw-r--r-- root/root 5368 2025-07-14 11:11 ./usr/share/samtools/test/split/split.sam -rw-r--r-- root/root 5575 2025-07-14 11:11 ./usr/share/samtools/test/split/split_d_nn.sam -rw-r--r-- root/root 3627 2025-07-14 11:11 ./usr/share/samtools/test/split/test_count_rg.c -rw-r--r-- root/root 6038 2025-07-14 11:11 ./usr/share/samtools/test/split/test_expand_format_string.c -rw-r--r-- root/root 9529 2025-07-14 11:11 ./usr/share/samtools/test/split/test_filter_header_rg.c -rw-r--r-- root/root 6828 2025-07-14 11:11 ./usr/share/samtools/test/split/test_parse_args.c drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/samtools/test/stat/ -rw-r--r-- root/root 66380 2025-07-14 11:11 ./usr/share/samtools/test/stat/1.stats.expected -rw-r--r-- root/root 47463 2025-07-14 11:11 ./usr/share/samtools/test/stat/1.stats.large.expected -rw-r--r-- root/root 66094 2025-07-14 11:11 ./usr/share/samtools/test/stat/10.stats.expected -rw-r--r-- root/root 433 2025-07-14 11:11 ./usr/share/samtools/test/stat/10_map_cigar.sam -rw-r--r-- root/root 66380 2025-07-14 11:11 ./usr/share/samtools/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat -rw-r--r-- root/root 66380 2025-07-14 11:11 ./usr/share/samtools/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat -rw-r--r-- root/root 8614 2025-07-14 11:11 ./usr/share/samtools/test/stat/11.stats.expected -rw-r--r-- root/root 8613 2025-07-14 11:11 ./usr/share/samtools/test/stat/11.stats.g4.expected -rw-r--r-- root/root 1162 2025-07-14 11:11 ./usr/share/samtools/test/stat/11.stats.targets -rw-r--r-- root/root 1937 2025-07-14 11:11 ./usr/share/samtools/test/stat/11_target.bam -rw-r--r-- root/root 192 2025-07-14 11:11 ./usr/share/samtools/test/stat/11_target.bam.bai -rw-r--r-- root/root 4546 2025-07-14 11:11 ./usr/share/samtools/test/stat/11_target.sam -rw-r--r-- root/root 42468 2025-07-14 11:11 ./usr/share/samtools/test/stat/12.2reads.nooverlap.expected -rw-r--r-- root/root 42483 2025-07-14 11:11 ./usr/share/samtools/test/stat/12.2reads.overlap.expected -rw-r--r-- root/root 41974 2025-07-14 11:11 ./usr/share/samtools/test/stat/12.3reads.nooverlap.expected -rw-r--r-- root/root 41988 2025-07-14 11:11 ./usr/share/samtools/test/stat/12.3reads.overlap.expected -rw-r--r-- root/root 21 2025-07-14 11:11 ./usr/share/samtools/test/stat/12_2reads.bed -rw-r--r-- root/root 21 2025-07-14 11:11 ./usr/share/samtools/test/stat/12_3reads.bed -rw-r--r-- root/root 1176 2025-07-14 11:11 ./usr/share/samtools/test/stat/12_overlaps.bam -rw-r--r-- root/root 11147 2025-07-14 11:11 ./usr/share/samtools/test/stat/13.barcodes.bc.ok.expected -rw-r--r-- root/root 13631 2025-07-14 11:11 ./usr/share/samtools/test/stat/13.barcodes.ox.ok.expected -rw-r--r-- root/root 330764 2025-07-14 11:11 ./usr/share/samtools/test/stat/13_barcodes_fail_bc_length.sam -rw-r--r-- root/root 330763 2025-07-14 11:11 ./usr/share/samtools/test/stat/13_barcodes_fail_hyphen.sam -rw-r--r-- root/root 330764 2025-07-14 11:11 ./usr/share/samtools/test/stat/13_barcodes_fail_qt_length.sam -rw-r--r-- root/root 330763 2025-07-14 11:11 ./usr/share/samtools/test/stat/13_barcodes_ok.sam -rw-r--r-- root/root 392771 2025-07-14 11:11 ./usr/share/samtools/test/stat/13_barcodes_ok_ox_bz.sam -rw-r--r-- root/root 8522 2025-07-14 11:11 ./usr/share/samtools/test/stat/14.rg.Sample.expected -rw-r--r-- root/root 8368 2025-07-14 11:11 ./usr/share/samtools/test/stat/14.rg.grp2.expected -rw-r--r-- root/root 4507 2025-07-14 11:11 ./usr/share/samtools/test/stat/14.rg.grp3.expected -rw-r--r-- root/root 47463 2025-07-14 11:11 ./usr/share/samtools/test/stat/14.rg.s1.expected -rw-r--r-- root/root 213 2025-07-14 11:11 ./usr/share/samtools/test/stat/15.big_del.sam -rw-r--r-- root/root 15358 2025-07-14 11:11 ./usr/share/samtools/test/stat/15.stats.expected -rw-r--r-- root/root 232 2025-07-14 11:11 ./usr/share/samtools/test/stat/1_map_cigar.sam -rw-r--r-- root/root 66380 2025-07-14 11:11 ./usr/share/samtools/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat -rw-r--r-- root/root 278 2025-07-14 11:11 ./usr/share/samtools/test/stat/1_map_cigar_large.sam -rw-r--r-- root/root 66380 2025-07-14 11:11 ./usr/share/samtools/test/stat/2.stats.expected -rw-r--r-- root/root 47463 2025-07-14 11:11 ./usr/share/samtools/test/stat/2.stats.large.expected -rw-r--r-- root/root 232 2025-07-14 11:11 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq.sam -rw-r--r-- root/root 278 2025-07-14 11:11 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq_large.sam -rw-r--r-- root/root 61277 2025-07-14 11:11 ./usr/share/samtools/test/stat/3.stats.expected -rw-r--r-- root/root 42360 2025-07-14 11:11 ./usr/share/samtools/test/stat/3.stats.large.expected -rw-r--r-- root/root 232 2025-07-14 11:11 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq.sam -rw-r--r-- root/root 278 2025-07-14 11:11 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq_large.sam -rw-r--r-- root/root 66380 2025-07-14 11:11 ./usr/share/samtools/test/stat/4.stats.expected -rw-r--r-- root/root 47463 2025-07-14 11:11 ./usr/share/samtools/test/stat/4.stats.large.expected -rw-r--r-- root/root 234 2025-07-14 11:11 ./usr/share/samtools/test/stat/4_X_cigar_full_seq.sam -rw-r--r-- root/root 280 2025-07-14 11:11 ./usr/share/samtools/test/stat/4_X_cigar_full_seq_large.sam -rw-r--r-- root/root 66402 2025-07-14 11:11 ./usr/share/samtools/test/stat/5.stats.expected -rw-r--r-- root/root 47485 2025-07-14 11:11 ./usr/share/samtools/test/stat/5.stats.large.expected -rw-r--r-- root/root 236 2025-07-14 11:11 ./usr/share/samtools/test/stat/5_insert_cigar.sam -rw-r--r-- root/root 282 2025-07-14 11:11 ./usr/share/samtools/test/stat/5_insert_cigar_large.sam -rw-r--r-- root/root 66402 2025-07-14 11:11 ./usr/share/samtools/test/stat/6.stats.expected -rw-r--r-- root/root 66416 2025-07-14 11:11 ./usr/share/samtools/test/stat/7.stats.expected -rw-r--r-- root/root 47499 2025-07-14 11:11 ./usr/share/samtools/test/stat/7.stats.large.expected -rw-r--r-- root/root 301 2025-07-14 11:11 ./usr/share/samtools/test/stat/7_supp.sam -rw-r--r-- root/root 366 2025-07-14 11:11 ./usr/share/samtools/test/stat/7_supp_large.sam -rw-r--r-- root/root 66402 2025-07-14 11:11 ./usr/share/samtools/test/stat/8.stats.expected -rw-r--r-- root/root 47485 2025-07-14 11:11 ./usr/share/samtools/test/stat/8.stats.large.expected -rw-r--r-- root/root 328 2025-07-14 11:11 ./usr/share/samtools/test/stat/8_secondary.sam -rw-r--r-- root/root 393 2025-07-14 11:11 ./usr/share/samtools/test/stat/8_secondary_large.sam -rw-r--r-- root/root 66380 2025-07-14 11:11 ./usr/share/samtools/test/stat/9.stats.expected -rw-r--r-- root/root 109 2025-07-14 11:11 ./usr/share/samtools/test/stat/test.fa -rw-r--r-- root/root 18 2025-07-14 11:11 ./usr/share/samtools/test/stat/test.fa.fai -rw-r--r-- root/root 2803 2025-07-14 11:11 ./usr/share/samtools/test/test.c -rw-r--r-- root/root 1466 2025-07-14 11:11 ./usr/share/samtools/test/test.h -rwxr-xr-x root/root 199009 2025-08-17 19:29 ./usr/share/samtools/test/test.pl drwxr-xr-x root/root 0 2025-07-14 11:11 ./usr/share/samtools/test/tview/ -rw-r--r-- root/root 2445 2025-07-14 11:11 ./usr/share/samtools/test/tview/test_get_rg_sample.c -rw-r--r-- root/root 3405 2025-07-14 11:11 ./usr/share/samtools/test/vcf-miniview.c samtools_1.22.1-1_amd64.deb --------------------------- new Debian package, version 2.0. size 697968 bytes: control archive=2972 bytes. 839 bytes, 17 lines control 5751 bytes, 84 lines md5sums Package: samtools Version: 1.22.1-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1502 Depends: libc6 (>= 2.38), libhts3t64 (>= 1.22.1), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.1.4) Suggests: cwltool Section: science Priority: optional Homepage: https://www.htslib.org/ Description: processing sequence alignments in SAM, BAM and CRAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing, and allows one to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP or HTTP server. drwxr-xr-x root/root 0 2025-08-17 19:29 ./ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/bin/ -rwxr-xr-x root/root 26856 2025-08-17 19:29 ./usr/bin/ace2sam -rwxr-xr-x root/root 5443 2025-08-17 19:29 ./usr/bin/blast2sam.pl -rwxr-xr-x root/root 3360 2025-08-17 19:29 ./usr/bin/bowtie2sam.pl -rwxr-xr-x root/root 17996 2025-08-17 19:29 ./usr/bin/export2sam.pl -rwxr-xr-x root/root 3300 2025-08-17 19:29 ./usr/bin/fasta-sanitize.pl -rwxr-xr-x root/root 6121 2025-08-17 19:29 ./usr/bin/interpolate_sam.pl -rwxr-xr-x root/root 14568 2025-08-17 19:29 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 14568 2025-08-17 19:29 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 14568 2025-08-17 19:29 ./usr/bin/md5fa -rwxr-xr-x root/root 14568 2025-08-17 19:29 ./usr/bin/md5sum-lite -rwxr-xr-x root/root 7969 2025-08-17 19:29 ./usr/bin/novo2sam.pl -rwxr-xr-x root/root 44331 2025-08-17 19:29 ./usr/bin/plot-ampliconstats -rwxr-xr-x root/root 59239 2025-08-17 19:29 ./usr/bin/plot-bamstats -rwxr-xr-x root/root 3204 2025-08-17 19:29 ./usr/bin/psl2sam.pl -rwxr-xr-x root/root 8957 2025-08-17 19:29 ./usr/bin/sam2vcf.pl -rwxr-xr-x root/root 836976 2025-08-17 19:29 ./usr/bin/samtools -rwxr-xr-x root/root 16474 2025-08-17 19:29 ./usr/bin/samtools.pl -rwxr-xr-x root/root 11337 2025-08-17 19:29 ./usr/bin/seq_cache_populate.pl -rwxr-xr-x root/root 3905 2025-08-17 19:29 ./usr/bin/soap2sam.pl -rwxr-xr-x root/root 22800 2025-08-17 19:29 ./usr/bin/wgsim -rwxr-xr-x root/root 12542 2025-08-17 19:29 ./usr/bin/wgsim_eval.pl -rwxr-xr-x root/root 3579 2025-08-17 19:29 ./usr/bin/zoom2sam.pl drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/ drwxr-xr-x root/root 0 2025-08-17 19:29 ./usr/share/commonwl/ -rwxr-xr-x root/root 1906 2025-08-17 19:27 ./usr/share/commonwl/samtools-faidx.cwl -rwxr-xr-x root/root 1979 2025-08-17 19:27 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./usr/share/man/man1/samtools-sort.1.gz -rw-r--r-- root/root 2798 2025-08-17 19:29 ./usr/share/man/man1/samtools-split.1.gz -rw-r--r-- root/root 6631 2025-08-17 19:29 ./usr/share/man/man1/samtools-stats.1.gz -rw-r--r-- root/root 1427 2025-08-17 19:29 ./usr/share/man/man1/samtools-targetcut.1.gz -rw-r--r-- root/root 2047 2025-08-17 19:29 ./usr/share/man/man1/samtools-tview.1.gz -rw-r--r-- root/root 7710 2025-08-17 19:29 ./usr/share/man/man1/samtools-view.1.gz -rw-r--r-- root/root 16963 2025-08-17 19:29 ./usr/share/man/man1/samtools.1.gz -rw-r--r-- root/root 410 2025-08-17 19:29 ./usr/share/man/man1/samtools.pl.1.gz -rw-r--r-- root/root 518 2025-08-17 19:29 ./usr/share/man/man1/wgsim.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 29 Jun 2026 22:06:22 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 29 Jun 2026 22:06:22 +0000 | +------------------------------------------------------------------------------+ Purging /build/samtools-V4kjE7 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 29 Jun 2026 22:06:22 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 59256 Build-Time: 69 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/samtools_1.22.1-1.dsc Machine Architecture: amd64 Package: samtools Package-Time: 85 Source-Version: 1.22.1-1 Space: 59256 Status: successful Version: 1.22.1-1 -------------------------------------------------------------------------------- Finished at 2026-06-29T22:06:21Z Build needed 00:01:25, 59256k disk space