sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | samtools 1.20-3 (amd64) Mon, 05 Aug 2024 01:11:52 +0000 | +==============================================================================+ Package: samtools Version: 1.20-3 Source Version: 1.20-3 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-a2cb08c4-6d3f-4a88-ab9e-f391afc16782' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup samtools_1.20-3 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup samtools_1.20-3 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/samtools-TC1nGO/resolver-LZBIHs' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] 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 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/samtools_1.20-3.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/samtools-TC1nGO/samtools-1.20' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-TC1nGO' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.20~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.20~), zlib1g-dev, automake, autoconf-archive, pkgconf, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [781 B] Get:5 copy:/<>/apt_archive ./ Packages [802 B] Fetched 2192 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... The following additional packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 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 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sensible-utils tabix zlib1g-dev Suggested packages: gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-doc krb5-user liblzma-doc ncurses-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx 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 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 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 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 38.0 MB/38.0 MB of archives. After this operation, 143 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20220903-3 [775 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 bash-completion all 1:2.14.0-1 [305 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 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libssl-dev amd64 3.3.1-2 [2739 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.0-7 [357 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.9.1-1 [582 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2 [349 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-1 [483 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.0 MB in 1s (75.1 MB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 22966 files and directories currently installed.) Preparing to unpack .../00-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package bash-completion. Preparing to unpack .../02-bash-completion_1%3a2.14.0-1_all.deb ... Unpacking bash-completion (1:2.14.0-1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... 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Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.16) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.62.1-2) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libpsl-dev:amd64 (0.21.2-1.1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up fakeroot (1.35.1-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.20.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up bash-completion (1:2.14.0-1) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libssl-dev:amd64 (3.3.1-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2) ... Setting up autoconf (2.71-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1) ... Setting up liblzma-dev:amd64 (5.6.2-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b2) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up tabix (1.20+ds-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libncurses-dev:amd64 (6.5-2) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libssh2-1-dev:amd64 (1.11.0-7) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.62.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-1) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up debhelper (13.16) ... Setting up libcurl4-gnutls-dev:amd64 (8.9.1-1) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 bash-completion_1:2.14.0-1 binutils_2.42.90.20240720-2 binutils-common_2.42.90.20240720-2 binutils-x86-64-linux-gnu_2.42.90.20240720-2 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-4 cpp-13-x86-64-linux-gnu_13.3.0-4 cpp-14_14.2.0-1 cpp-14-x86-64-linux-gnu_14.2.0-1 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 g++-14_14.2.0-1 g++-14-x86-64-linux-gnu_14.2.0-1 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-4 gcc-13-base_13.3.0-4 gcc-13-x86-64-linux-gnu_13.3.0-4 gcc-14_14.2.0-1 gcc-14-base_14.2.0-1 gcc-14-x86-64-linux-gnu_14.2.0-1 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8 gpg_2.2.43-8 gpg-agent_2.2.43-8 gpg-wks-client_2.2.43-8 gpgconf_2.2.43-8 gpgsm_2.2.43-8 gpgv_2.2.43-8 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.7 libarchive-zip-perl_1.68-1 libasan8_14.2.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.2.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-4 libaudit1_1:3.1.2-4+b1 libbinutils_2.42.90.20240720-2 libblkid1_2.40.2-1 libbrotli-dev_1.1.0-2+b4 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libbz2-dev_1.0.8-5.1 libc-bin_2.39-6 libc-dev-bin_2.39-6 libc-l10n_2.39-6 libc6_2.39-6 libc6-dev_2.39-6 libcap-ng0_0.8.5-1+b1 libcap2_1:2.66-5 libcc1-0_14.2.0-1 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42.90.20240720-2 libctf0_2.42.90.20240720-2 libcurl3t64-gnutls_8.9.1-1 libcurl4-gnutls-dev_8.9.1-1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdeflate-dev_1.20-1 libdeflate0_1.20-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libevent-2.1-7t64_2.1.12-stable-10 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-4 libgcc-14-dev_14.2.0-1 libgcc-s1_14.2.0-1 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp-dev_2:6.3.0+dfsg-2+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgmpxx4ldbl_2:6.3.0+dfsg-2+b1 libgnutls-dane0t64_3.8.6-2 libgnutls-openssl27t64_3.8.6-2 libgnutls28-dev_3.8.6-2 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.50-2 libgprofng0_2.42.90.20240720-2 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts-dev_1.20+ds-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14.2.0-1 libicu72_72.1-5 libidn2-0_2.3.7-2 libidn2-dev_2.3.7-2 libio-pty-perl_1:1.20-1+b2 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2+b1 liblsan0_14.2.0-1 liblz4-1_1.9.4-3 liblzma-dev_5.6.2-2 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncurses-dev_6.5-2 libncurses6_6.5-2 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.62.1-2 libnghttp2-dev_1.62.1-2 libnghttp3-9_1.4.0-1 libnghttp3-dev_1.4.0-1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls-dev_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libngtcp2-dev_1.6.0-1 libnpth0t64_1.6-3.1 libp11-kit-dev_0.25.5-2 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-1 libpipeline1_1.5.7-2 libpkgconf3_1.8.1-3 libpsl-dev_0.21.2-1.1 libpsl5t64_0.21.2-1.1 libquadmath0_14.2.0-1 libreadline8t64_8.2-4 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b4 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b3 libsemanage-common_3.5-1 libsemanage2_3.5-1+b4 libsepol2_3.5-2+b1 libsframe1_2.42.90.20240720-2 libsmartcols1_2.40.2-1 libsqlite3-0_3.46.0-1 libssh2-1-dev_1.11.0-7 libssh2-1t64_1.11.0-7 libssl-dev_3.3.1-2 libssl3t64_3.3.1-2 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 libtasn1-6-dev_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-1 libubsan1_14.2.0-1 libuchardet0_0.0.8-1+b1 libudev1_256.4-2 libunbound8_1.20.0-1+b1 libunistring5_1.2-1 libuuid1_2.40.2-1 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd-dev_1.5.6+dfsg-1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.9.12-1 locales-all_2.39-6 login_1:4.15.3-3 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240622-2 ncurses-base_6.5-2 ncurses-bin_6.5-2 nettle-dev_3.10-1 passwd_1:4.15.3-3 patch_2.7.6-7 perl_5.40.0-1 perl-base_5.40.0-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-1 pinentry-curses_1.2.1-3+b2 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.09-2 tabix_1.20+ds-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.20-3 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.7.0 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 (>= 1.20~), 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: 2b83ecc36ffcd39871749e840930c4eb0cdb70cf 5682525 samtools_1.20.orig.tar.gz e539b922b2610d9838682a4aa015bf2e72bbf3ae 22020 samtools_1.20-3.debian.tar.xz Checksums-Sha256: d0ca264732c2897ba85839e65e19cef0c5e1c19f54f4cd8e4ee10c07e3e1d20a 5682525 samtools_1.20.orig.tar.gz 4e6bb7814b0a360dac463c2e80868f1797158465d9c42bcb52580ef118c64641 22020 samtools_1.20-3.debian.tar.xz Files: 2c4b7e07bd7c1fce1e060a9039b27818 5682525 samtools_1.20.orig.tar.gz 5bf195cc49a1de89b804d215113d9158 22020 samtools_1.20-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZYzCAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdo0ww/+N1jO38yIrIbXlXhBJmCL+Le8GkR/ btt6j3rQ88rEAFmBxzsFri0LJ0hzcXnZtOJhSN8FN7ftmiWDbIUq+792odmlJCxV vmXlb9UzFW4+wdiuGEXvYjyz/vPkmxbXV2/e5EvdeBP0+A/ecVWmZlYS6itw74Xu wzKoabm1ztsvmnl3rLQ8doLCu0s8GuICQfN7EOTtEoqlwUiuzjguYRwZX1Qb6SaB 31fQ4dnvjRNC6j+e3z4Jk1kTASDqi9OCp+cVmUu1bOQBD0VcAiQ5CFJPRnEjuCJs D7Bka5HHtG5urgoOv0vdGEuYk7mlk4LUOnSybHjphhNvc3VVi3JWnf80zr5RLWuO NfdewfrspyaL3ouBz76TQDvrrHoEY81nEM3pfu41otUiH2RnUQQ1nOP2Qn+AFxvP dINeX0VAwtPmHqyuwsExULwWc73j+j4AITpYALtB+X8R/bfdhtkRB7GNaYcvsvE4 feWgHwn77+YvCHjwRgmI6d/8vW1f9tEvjXrl6uqtwrTrmr4gcTfAyU603/ape7nG r8csaO7hTCE5vL737iBUuPoKjSUipEgK//vXdTxXjCG0MHCUfdWPMBtH7x9r9yGU cWhy+EzCHrlwB7fS2oN+acl30aC1ALgGU1B2jtHI7wpW4bEsDlzxVWT+WA2MUjOo jSw/5L4Fp6A3lho= =eAPr -----END PGP SIGNATURE----- gpgv: Signature made Thu May 30 18:57:36 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.20-3.dsc: no acceptable signature found dpkg-source: info: extracting samtools in /<> dpkg-source: info: unpacking samtools_1.20.orig.tar.gz dpkg-source: info: unpacking samtools_1.20-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network samtools_1.20-3 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network samtools_1.20-3 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 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=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-a2cb08c4-6d3f-4a88-ab9e-f391afc16782 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.20-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from samtools-1.20/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 '/<>' rm -f config.mk touch config.mk dh_auto_clean -- make -j2 distclean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* 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 '/<>' make[1]: Leaving directory '/<>' 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 samtools-1.20/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_1.20.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building samtools in samtools_1.20-3.debian.tar.xz dpkg-source: info: building samtools in samtools_1.20-3.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 configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=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... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no 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 '/<>' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/<>' 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=/<>=. -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 '/<>' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 "1.20"' > version.h echo '#define SAMTOOLS_CC "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=/<>=. -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@/<>@«BUILDPATH»@g' version.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -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 gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j2 test "TESTSUITEFLAGS=-j2 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/<>' 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: /<>/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/1KUy9II0tg/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/1KUy9II0tg/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/1KUy9II0tg/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/1KUy9II0tg/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq.gz 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq.gz 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq.gz 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq 1:99998-100007 .. ok .. ok /<>/samtools fqidx /tmp/1KUy9II0tg/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /<>/test/dat/dict.fa .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/1KUy9II0tg/dict.fa.gz .. ok test_dict: cat /<>/test/dat/dict.fa | /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /<>/samtools dict -AH < /<>/test/dat/dict.alias.fa .. ok test_dict: /<>/samtools dict -H -l /<>/test/dat/dict.alt < /<>/test/dat/dict.alias.fa .. ok test_index: /<>/samtools view /tmp/1KUy9II0tg/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/1KUy9II0tg/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/1KUy9II0tg/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/1KUy9II0tg/test_input_1_b.bam.bai .. ok test_index: /<>/samtools merge -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/1KUy9II0tg/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/1KUy9II0tg/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam .. ok test_index: /<>/samtools index -M /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.bam /tmp/1KUy9II0tg/auto_indexed.csi && cat /tmp/1KUy9II0tg/auto_indexed.csi .. ok test_index: /<>/samtools index /<>/test/dat/auto_indexed.tmp.cram /tmp/1KUy9II0tg/auto_indexed.crai && cat /tmp/1KUy9II0tg/auto_indexed.crai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.sam /tmp/1KUy9II0tg/auto_indexed.csi && cat /tmp/1KUy9II0tg/auto_indexed.csi .. ok test_index: /<>/samtools view -@ 2 /tmp/1KUy9II0tg/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/1KUy9II0tg/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/1KUy9II0tg/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/1KUy9II0tg/test_input_1_b.bam.bai .. ok test_index: /<>/samtools merge -@ 2 -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/1KUy9II0tg/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/1KUy9II0tg/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam .. ok test_index: /<>/samtools index -@ 2 -M /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.bam /tmp/1KUy9II0tg/auto_indexed.csi && cat /tmp/1KUy9II0tg/auto_indexed.csi .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/auto_indexed.tmp.cram /tmp/1KUy9II0tg/auto_indexed.crai && cat /tmp/1KUy9II0tg/auto_indexed.crai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.sam /tmp/1KUy9II0tg/auto_indexed.csi && cat /tmp/1KUy9II0tg/auto_indexed.csi .. ok test_mpileup: /<>/samtools mpileup -b /tmp/1KUy9II0tg/mpileup.bam.list -f /tmp/1KUy9II0tg/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/1KUy9II0tg/mpileup.cram.list -f /tmp/1KUy9II0tg/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/1KUy9II0tg/mpileup.bam.urllist -f /tmp/1KUy9II0tg/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/1KUy9II0tg/mpileup.cram.urllist -f /tmp/1KUy9II0tg/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/1KUy9II0tg/mpileup.ref.fa.gz -r17:1050-1060 /tmp/1KUy9II0tg/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/1KUy9II0tg/mpileup.ref.fa.gz -r17:1050-1060 /tmp/1KUy9II0tg/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup /<>/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate .. ok test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools reset .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/1KUy9II0tg/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/1KUy9II0tg/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/1KUy9II0tg/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/1KUy9II0tg/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/1KUy9II0tg/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/1KUy9II0tg/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/1KUy9II0tg/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/1KUy9II0tg/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/1KUy9II0tg/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/1KUy9II0tg/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/1KUy9II0tg/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/1KUy9II0tg/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/1KUy9II0tg/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/1KUy9II0tg/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/1KUy9II0tg/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/1KUy9II0tg/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/1KUy9II0tg/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/1KUy9II0tg/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/1KUy9II0tg/view.001.forn (SAM input) .. ok 68: Count -N /tmp/1KUy9II0tg/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/1KUy9II0tg/view.001.forn (BAM input) .. ok 70: Count -N /tmp/1KUy9II0tg/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/1KUy9II0tg/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/1KUy9II0tg/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/1KUy9II0tg/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/1KUy9II0tg/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/1KUy9II0tg/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/1KUy9II0tg/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/1KUy9II0tg/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/1KUy9II0tg/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/1KUy9II0tg/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/1KUy9II0tg/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/1KUy9II0tg/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/1KUy9II0tg/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/1KUy9II0tg/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/1KUy9II0tg/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/1KUy9II0tg/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/1KUy9II0tg/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/1KUy9II0tg/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/1KUy9II0tg/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/1KUy9II0tg/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/1KUy9II0tg/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/1KUy9II0tg/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/1KUy9II0tg/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/1KUy9II0tg/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/1KUy9II0tg/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/1KUy9II0tg/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/1KUy9II0tg/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: /<>/samtools view -o /tmp/1KUy9II0tg/view.test115.sam -h -d TGCA /tmp/1KUy9II0tg/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/1KUy9II0tg/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/1KUy9II0tg/view.test117.sam -h -d TGCA /tmp/1KUy9II0tg/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/1KUy9II0tg/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/1KUy9II0tg/view.test119.sam -h -d TGCA /tmp/1KUy9II0tg/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/1KUy9II0tg/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/1KUy9II0tg/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/1KUy9II0tg/view.001.fobc" Failed command: /<>/samtools view -o /tmp/1KUy9II0tg/view.test121.sam -h -D BClong:/tmp/1KUy9II0tg/view.001.fobc /tmp/1KUy9II0tg/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/1KUy9II0tg/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/1KUy9II0tg/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/1KUy9II0tg/view.001.fobc /tmp/1KUy9II0tg/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/1KUy9II0tg/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/1KUy9II0tg/view.001.fobc" Failed command: /<>/samtools view -o /tmp/1KUy9II0tg/view.test123.sam -h -D BClong:/tmp/1KUy9II0tg/view.001.fobc /tmp/1KUy9II0tg/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/1KUy9II0tg/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/1KUy9II0tg/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/1KUy9II0tg/view.001.fobc /tmp/1KUy9II0tg/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/1KUy9II0tg/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/1KUy9II0tg/view.001.fobc" Failed command: /<>/samtools view -o /tmp/1KUy9II0tg/view.test125.sam -h -D BClong:/tmp/1KUy9II0tg/view.001.fobc /tmp/1KUy9II0tg/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/1KUy9II0tg/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/1KUy9II0tg/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/1KUy9II0tg/view.001.fobc /tmp/1KUy9II0tg/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: /<>/samtools view -o /tmp/1KUy9II0tg/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/1KUy9II0tg/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: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/1KUy9II0tg/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: /<>/samtools view -o /tmp/1KUy9II0tg/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/1KUy9II0tg/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: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/1KUy9II0tg/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: /<>/samtools view -o /tmp/1KUy9II0tg/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/1KUy9II0tg/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: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/1KUy9II0tg/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 /<>/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /<>/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /<>/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /<>/test/dat/view.001.03.bed (BAM input).. ok 351: Count -L /<>/test/dat/view.001.03.bed (BAM input).. ok 352: Region -L /<>/test/dat/view.001.03.bed (CRAM input).. ok 353: Count -L /<>/test/dat/view.001.03.bed (CRAM input).. ok 354: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 355: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 356: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 357: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 358: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 359: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 360: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 361: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 362: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 363: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 364: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 365: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 366: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 367: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 368: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 369: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 370: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 371: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 372: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 373: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 374: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 375: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 376: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 377: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 378: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 379: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 380: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 381: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 382: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 383: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 384: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 385: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 386: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 387: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 388: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 389: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 390: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 391: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 392: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 393: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 394: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 395: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 396: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 397: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 398: Region -L /<>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 399: Count -L /<>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 400: Region -L /<>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 401: Count -L /<>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 402: Region -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 403: Count -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 404: Region -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 405: Count -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 406: Make BAM with no M5/UR tags .. ok 407: Add @SQ with -t (SAM -> SAM) .. ok 408: Add @SQ with -T (SAM -> SAM) .. ok 409: Add @SQ with -t (BAM -> SAM) .. ok 410: Add @SQ with -T (BAM -> SAM) .. ok 411: Add @SQ with -t (SAM -> BAM) .. ok 412: Add @SQ with -T (SAM -> BAM) .. ok 413: Add @SQ with -t (BAM -> BAM) .. ok 414: Add @SQ with -T (BAM -> BAM) .. ok 415: Add @SQ with -t (SAM -> CRAM) .. ok 416: Add @SQ with -T (SAM -> CRAM) .. ok 417: Add @SQ with -t (BAM -> CRAM) .. ok 418: Add @SQ with -T (BAM -> CRAM) .. ok 419: Make CRAM with no UR field .. ok 420: Decoding CRAM with no UR field via -T .. ok 421: CIGAR B-operator removal .. ok 422: Big SAM -> BAM .. ok 423: Big SAM -> BAM (2 threads) .. ok 424: Big SAM -> BAM (4 threads) .. ok 425: Big SAM -> CRAM .. ok 426: Big SAM -> CRAM (2 threads) .. ok 427: Big SAM -> CRAM (4 threads) .. ok 428: Subsample 0.2 (SAM input) ............ ok 429: Subsample 0.5 (SAM input) ............ ok 430: Subsample 0.8 (SAM input) ............ ok 431: Subsample 0.2 (BAM input) ............ ok 432: Subsample 0.5 (BAM input) ............ ok 433: Subsample 0.8 (BAM input) ............ ok 434: Subsample 0.2 (CRAM input) ............ ok 435: Subsample 0.5 (CRAM input) ............ ok 436: Subsample 0.8 (CRAM input) ............ ok 437: SAM add PG .. ok 438: Unset dup flag, remove dt and do tags .. ok 439: Unmap dup flagged reads. .. ok 440: Unmap dup flagged reads. .. ok 441: fetch pairs .. ok 442: fetch pairs .. ok 443: fetch pairs .. ok test_head: /<>/samtools head /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 0 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 1 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 5 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 29 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 30 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 0 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 1 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 5 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 5 -n 5 < /<>/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM 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 BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /<>/samtools import --no-PG -0 test/bam2fq/1.1.fq.expected | /<>/samtools fastq -0 /<>/test/0.fq .. ok test_import: /<>/samtools import --no-PG -s test/bam2fq/1.1.fq.expected | /<>/samtools fastq -0 /<>/test/0.fq .. ok test_import: /<>/samtools import --no-PG -s test/bam2fq/5.s.fq.expected | /<>/samtools fastq -s /<>/test/s.fq .. ok test_import: /<>/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --no-PG test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /<>/samtools fastq -N -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --no-PG -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<>/samtools fastq -i --index-format 'i*i*' -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --no-PG --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<>/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --no-PG -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /<>/samtools fastq -N -T RG,BC,QT -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --no-PG -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /<>/samtools fastq -N -T RG,BC,QT,MD,ia -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /<>/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /<>/samtools import --no-PG test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /<>/samtools import --no-PG test/import/2.interleaved.fq -T "" .. ok test_import: /<>/samtools import --no-PG test/import/3.interleaved.fq -i .. ok test_import: /<>/samtools import --no-PG test/import/4.aux.fq -T "*" .. ok test_import: /<>/samtools import --no-PG test/import/4.aux.fq -T "" .. ok test_import: /<>/samtools import --no-PG test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /<>/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: /<>/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: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fasta -N -1 /<>/test/o.fa -2 /<>/test/o.fa /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -s /tmp/1KUy9II0tg/bam2fq.discard.s.fq -0 /tmp/1KUy9II0tg/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_bam2fq: /<>/samtools fastq --index-format 'i8n1i8' --i1 /<>/test/i1.fq --i2 /<>/test/i2.fq -0 /<>/test/0.fq /<>/test/dat/bam2fq.014.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '*' -d MD:10 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '*' -d NM:0 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '*' -d ia /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -d NM:13 -d NM:14 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -D NM:test/dat/bam2fq.NM-D /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -D MD:test/dat/bam2fq.MD-D /<>/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: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fasta -@ 2 -N -1 /<>/test/o.fa -2 /<>/test/o.fa /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -s /tmp/1KUy9II0tg/bam2fq.discard.s.fq -0 /tmp/1KUy9II0tg/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /<>/test/i1.fq --i2 /<>/test/i2.fq -0 /<>/test/0.fq /<>/test/dat/bam2fq.014.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '*' -d MD:10 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '*' -d NM:0 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '*' -d ia /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -d NM:13 -d NM:14 /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -D NM:test/dat/bam2fq.NM-D /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -D MD:test/dat/bam2fq.MD-D /<>/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: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa -i 0 /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats -I s1 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I grp2 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I grp3 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I Sample /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/mpileup/ce.fa /<>/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam -b /tmp/hbpAMTL5MK - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -o - -s 1 -O sam /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/1KUy9II0tg/merge.tag.1.bam /tmp/1KUy9II0tg/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/1KUy9II0tg/merge.tag.3.bam /tmp/1KUy9II0tg/merge.tag.4.bam .. ok test_merge: /<>/samtools merge --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/1KUy9II0tg/merge.bed.1.bam /tmp/1KUy9II0tg/merge.bed.2.bam .. ok test_merge: /<>/samtools merge --no-PG -r -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam -b /tmp/moqcDK74Ep - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -@ 2 -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -@ 2 -o - -s 1 -O sam /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/1KUy9II0tg/merge.tag.1.bam /tmp/1KUy9II0tg/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/1KUy9II0tg/merge.tag.3.bam /tmp/1KUy9II0tg/merge.tag.4.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/1KUy9II0tg/merge.bed.1.bam /tmp/1KUy9II0tg/merge.bed.2.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -r -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam /tmp/1KUy9II0tg/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/1KUy9II0tg/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/1KUy9II0tg/sorttmp .. ok test_sort: /<>/samtools sort -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -N -m 10M /<>/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -m 10M /<>/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort --template-coordinate -m 10M /<>/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -M -K10 -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -M -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -MH -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 /<>/test/dat/test_input_1_a.bam /tmp/1KUy9II0tg/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/1KUy9II0tg/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/1KUy9II0tg/sorttmp .. ok test_sort: /<>/samtools sort -@ 2 -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -N -m 10M /<>/test/dat/test_input_1_b.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -m 10M /<>/test/dat/sort_name_input_1.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 --template-coordinate -m 10M /<>/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -@ 2 -M -K10 -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -@ 2 -M -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_sort: /<>/samtools reset /<>/test/dat/auto_indexed.tmp.bam | /<>/samtools sort -@ 2 -MH -K10 -I /<>/test/dat/mpileup.ref.fa -O SAM -o - .. ok test_collate: /<>/samtools collate --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/sanitize.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_draft.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /<>/samtools fixmate -M -z off -O sam /<>/test/fixmate/mod_bounds.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/sanitize.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_ok+.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_ok-.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_draft.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_not_updated.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_not_updated_noML.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_not_updated_noMN.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_bad_MN.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_MN_only.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_ML_only.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_ML_wrong_len.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_noseq.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -M -z off -O sam /<>/test/fixmate/mod_bounds.sam - .. ok /<>/samtools calmd -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok /<>/samtools calmd -@ 2 -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.bam .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.cram .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.sam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /<>/samtools quickcheck -v /<>/test/quickcheck/1.quickcheck.badeof.bam /<>/test/quickcheck/2.quickcheck.badheader.bam /<>/test/quickcheck/3.quickcheck.ok.bam /<>/test/quickcheck/4.quickcheck.ok.bam /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<>/test/quickcheck/6.quickcheck.cram21.ok.cram /<>/test/quickcheck/7.quickcheck.cram30.ok.cram /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /<>/samtools quickcheck -uv /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<>/test/addrprg/1_fixup.sam .. ok test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/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: /<>/samtools markdup -O sam --no-PG /<>/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: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<>/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<>/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<>/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /<>/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 /<>/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /<>/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 /<>/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /<>/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /<>/test/markdup/17_read_group.sam - .. ok test_markdup: /<>/samtools markdup --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<>/test/markdup/18_primary_duplicate_count.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/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: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/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: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<>/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<>/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<>/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /<>/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 /<>/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /<>/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 /<>/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /<>/test/markdup/17_read_group.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 --mode t -t -O sam --no-PG --duplicate-count --barcode-tag BC -S /<>/test/markdup/18_primary_duplicate_count.sam - .. ok test_bedcov: /<>/samtools bedcov /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -j /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -g512 -G2048 /<>/test/bedcov/bedcov_gG.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -c /<>/test/bedcov/bedcov_gG.bed /<>/test/bedcov/bedcov.bam .. ok test_split: /<>/samtools split --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%#.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -p 5 -f /<>/test/split/split.tmp.%#.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -d RG -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -d an -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -d an -M 3 -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split --output-fmt sam -f /<>/test/split/split.tmp.d_nn.%!.%. -d nn -u /<>/test/split/split.tmp.d_nn.unk.sam /<>/test/split/split_d_nn.sam .. ok test_split: /<>/samtools split --output-fmt sam -f /<>/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /<>/test/split/split.tmp.d_nn.0unk.sam /<>/test/split/split_d_nn.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%#.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -p 5 -f /<>/test/split/split.tmp.%#.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -d RG -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -d an -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -d an -M 3 -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -f /<>/test/split/split.tmp.d_nn.%!.%. -d nn -u /<>/test/split/split.tmp.d_nn.unk.sam /<>/test/split/split_d_nn.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -f /<>/test/split/split.tmp.d_nn.%!.%. -p 4 -d nn -u /<>/test/split/split.tmp.d_nn.0unk.sam /<>/test/split/split_d_nn.sam .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/1KUy9II0tg/longref.sam.gz .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/1KUy9II0tg/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /<>/samtools view -h --no-PG -L /<>/test/large_pos/test.bed /tmp/1KUy9II0tg/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -m 10M /<>/test/large_pos/longref_name.sam .. ok test_large_positions: /<>/samtools merge -O sam --no-PG - /<>/test/large_pos/longref.sam /<>/test/large_pos/longref2.sam .. ok test_large_positions: /<>/samtools depth /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools depth -b /<>/test/large_pos/test.bed /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/1KUy9II0tg/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /<>/samtools fixmate -O sam --no-PG - - | /<>/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test2.bed /<>/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test2.bed /<>/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_hard_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped_strand.expected.sam /<>/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -c 0 /<>/test/ampliconclip/multi_ref.bed /<>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -c 0 /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /<>/test/dat/mpileup.1.sam | /<>/samtools reset | /<>/samtools view .. ok test_reset: /<>/samtools reset < /<>/test/dat/mpileup.1.sam | /<>/samtools view .. ok test_reset: /<>/samtools reset /<>/test/dat/mpileup.1.sam | /<>/samtools view .. ok test_reset: cat /<>/test/dat/mpileup.1.sam | /<>/samtools reset -o /<>/test/reset/output.tmp.sam .. ok test_reset: /<>/samtools reset -o /<>/test/reset/output.tmp.sam /<>/test/dat/test_input_1_a.bam .. ok test_reset: /<>/samtools reset -o /<>/test/reset/output.tmp.sam /<>/test/dat/test_input_1_a.cram .. ok test_reset: /<>/samtools reset --reject-PG bwa_index /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.tmp.sam; grep /<>/test/reset/output.tmp.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /<>/samtools reset --reject-PG sam_to_fixed_bam /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.tmp.sam; grep /<>/test/reset/output.tmp.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /<>/samtools reset --reject-PG bwa_index --no-PG /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.tmp.sam; grep /<>/test/reset/output.tmp.sam -e"@PG" .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset /<>/test/reset/seq.sam -o /<>/test/reset/output .. ok Number of tests: total .. 973 passed .. 929 failed .. 0 expected failure .. 44 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 120 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 53 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh cram-size.reg === Testing cram-size.reg regressions === Expected passes: 5 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 65 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/<>' rm -fr -- /tmp/dh-xdg-rundir-8GTkV72x make[1]: Leaving directory '/<>' 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 '/<>' dh_auto_install -- \ prefix=/usr install -m0755 -d /<>/debian/tmp make -j2 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/share/man/man1 install -p samtools /<>/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<>/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 /<>/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /<>/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/<>' make clean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* 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 '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools-test.debhelper.log debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>' 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 '/<>' 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 '/<>' 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 '/<>' 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 '/<>' # 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 '/<>' dh_installman rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 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-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-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 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 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 1717095173 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip Using 1717095173 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-test cd debian/samtools chmod a-x usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 chmod a-x usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian gzip -9nf 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-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 cd '/<>' cd '/<>' 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-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s 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/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 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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 '/<>' chmod -x /<>/debian/samtools-test/usr/share/samtools/test/mpileup/mp_2018.sam make[1]: Leaving directory '/<>' 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 809561 new size 832004 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/3d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3d/d375828b8cfe29a5ec0bcdbc21b8f5da4de266.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3d/d375828b8cfe29a5ec0bcdbc21b8f5da4de266.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/3d/d375828b8cfe29a5ec0bcdbc21b8f5da4de266.debug debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/32 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/32/abc2dd77ed20fd8a98345cd02122c2c6195c99.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/32/abc2dd77ed20fd8a98345cd02122c2c6195c99.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/32/abc2dd77ed20fd8a98345cd02122c2c6195c99.debug debian/samtools/usr/bin/md5sum-lite install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/03 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/03/af89567c606cee6e8b671ebce9c44b001edd1a.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/03/af89567c606cee6e8b671ebce9c44b001edd1a.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/03/af89567c606cee6e8b671ebce9c44b001edd1a.debug debian/samtools/usr/bin/ace2sam install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/532afb2e553e06457a2df1e884a7a75687332f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/532afb2e553e06457a2df1e884a7a75687332f.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/46/532afb2e553e06457a2df1e884a7a75687332f.debug debian/samtools/usr/bin/wgsim install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9a/f7cb05cf434355039fb11aaf4feee016ad62ab.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9a/f7cb05cf434355039fb11aaf4feee016ad62ab.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/9a/f7cb05cf434355039fb11aaf4feee016ad62ab.debug debian/samtools/usr/bin/md5fa install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/a7e81e438ae4c0fa54e5695030af7258738290.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/a7e81e438ae4c0fa54e5695030af7258738290.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/8d/a7e81e438ae4c0fa54e5695030af7258738290.debug debian/samtools/usr/bin/samtools install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/75 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/75/7cdf787b4b4d0f5c3cb3691c544aaa5605d643.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/75/7cdf787b4b4d0f5c3cb3691c544aaa5605d643.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/75/7cdf787b4b4d0f5c3cb3691c544aaa5605d643.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-test/DEBIAN echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -cdebian/control -Pdebian/samtools-test install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=03af89567c606cee6e8b671ebce9c44b001edd1a 32abc2dd77ed20fd8a98345cd02122c2c6195c99 3dd375828b8cfe29a5ec0bcdbc21b8f5da4de266 46532afb2e553e06457a2df1e884a7a75687332f 757cdf787b4b4d0f5c3cb3691c544aaa5605d643 8da7e81e438ae4c0fa54e5695030af7258738290 9af7cb05cf434355039fb11aaf4feee016ad62ab" -DSection=debug -UMulti-Arch -UReplaces -UBreaks 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/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -cdebian/control -Pdebian/samtools dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums install -m0755 -d debian/samtools/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/samtools-test/DEBIAN chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.20-3_all.deb'. dpkg-deb: building package 'samtools' in '../samtools_1.20-3_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root .. dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.20-3_amd64.deb'. dpkg-genbuildinfo -O../samtools_1.20-3_amd64.buildinfo dpkg-genchanges -O../samtools_1.20-3_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from samtools-1.20/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-08-05T01:13:30Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.20-3_amd64.changes: ------------------------------ Format: 1.8 Date: Thu, 30 May 2024 20:52:53 +0200 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: source amd64 all Version: 1.20-3 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats samtools-test - test files for the samtools package Changes: samtools (1.20-3) unstable; urgency=medium . * [56a4a28] d/rules: fix no-arch-all builds. The initial issue flown below radar due to leftover htslib version discrepancy, triggering the build failure too early. Checksums-Sha1: 24f3134c9ae9abb03780b275933099c638b73ccd 1369 samtools_1.20-3.dsc e539b922b2610d9838682a4aa015bf2e72bbf3ae 22020 samtools_1.20-3.debian.tar.xz 1a9b75127fcb65d82cc2c05081f05a6ed1eab95f 991576 samtools-dbgsym_1.20-3_amd64.deb 16035b5c40a5945e72a35fcc47a467464eb3b171 2364248 samtools-test_1.20-3_all.deb 71a3d4e3572a1c1db50cc23f283f9d328da10f57 7541 samtools_1.20-3_amd64.buildinfo 7794060cad159c6302ce1d8025e7de86968833b9 657552 samtools_1.20-3_amd64.deb Checksums-Sha256: 9753cb3662581e70c7a3115a02ed55d521a7abded601cd1f5d0a9b81eb595851 1369 samtools_1.20-3.dsc 4e6bb7814b0a360dac463c2e80868f1797158465d9c42bcb52580ef118c64641 22020 samtools_1.20-3.debian.tar.xz eb876b3d720f3d26f37d6deffe1d8b71877ea1527201b39ed726377ce16f729c 991576 samtools-dbgsym_1.20-3_amd64.deb 8c9c5ddf0aa46dc2e7b99f0eb12e659297bc90dd665156356b434b3637234ff4 2364248 samtools-test_1.20-3_all.deb 9e3132229e114c1572fad4036fe33350d1f2baf3b4f5d2625eb19f11bfd154da 7541 samtools_1.20-3_amd64.buildinfo a849fa159ec16d63c91050e1cce793ec27266d74174d5026d6f95116b13024f4 657552 samtools_1.20-3_amd64.deb Files: 26c76226499dd70c364d6374c7a58e03 1369 science optional samtools_1.20-3.dsc 5bf195cc49a1de89b804d215113d9158 22020 science optional samtools_1.20-3.debian.tar.xz 4586321040f978dffef6d22391b952f3 991576 debug optional samtools-dbgsym_1.20-3_amd64.deb 828d763364c1eeb129440bdf139ba5f1 2364248 science optional samtools-test_1.20-3_all.deb 863fc1512d8713c71478c27faaabd407 7541 science optional samtools_1.20-3_amd64.buildinfo e6708f9096408516aac474a8cc433057 657552 science optional samtools_1.20-3_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools Binary: samtools samtools-dbgsym samtools-test Architecture: all amd64 source Version: 1.20-3 Checksums-Md5: 26c76226499dd70c364d6374c7a58e03 1369 samtools_1.20-3.dsc 4586321040f978dffef6d22391b952f3 991576 samtools-dbgsym_1.20-3_amd64.deb 828d763364c1eeb129440bdf139ba5f1 2364248 samtools-test_1.20-3_all.deb e6708f9096408516aac474a8cc433057 657552 samtools_1.20-3_amd64.deb Checksums-Sha1: 24f3134c9ae9abb03780b275933099c638b73ccd 1369 samtools_1.20-3.dsc 1a9b75127fcb65d82cc2c05081f05a6ed1eab95f 991576 samtools-dbgsym_1.20-3_amd64.deb 16035b5c40a5945e72a35fcc47a467464eb3b171 2364248 samtools-test_1.20-3_all.deb 7794060cad159c6302ce1d8025e7de86968833b9 657552 samtools_1.20-3_amd64.deb Checksums-Sha256: 9753cb3662581e70c7a3115a02ed55d521a7abded601cd1f5d0a9b81eb595851 1369 samtools_1.20-3.dsc eb876b3d720f3d26f37d6deffe1d8b71877ea1527201b39ed726377ce16f729c 991576 samtools-dbgsym_1.20-3_amd64.deb 8c9c5ddf0aa46dc2e7b99f0eb12e659297bc90dd665156356b434b3637234ff4 2364248 samtools-test_1.20-3_all.deb a849fa159ec16d63c91050e1cce793ec27266d74174d5026d6f95116b13024f4 657552 samtools_1.20-3_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 05 Aug 2024 01:13:29 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), autoconf-archive (= 20220903-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.4), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), bash-completion (= 1:2.14.0-1), binutils (= 2.42.90.20240720-2), binutils-common (= 2.42.90.20240720-2), binutils-x86-64-linux-gnu (= 2.42.90.20240720-2), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-4), cpp-13-x86-64-linux-gnu (= 13.3.0-4), cpp-14 (= 14.2.0-1), cpp-14-x86-64-linux-gnu (= 14.2.0-1), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-2), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-1), g++-14-x86-64-linux-gnu (= 14.2.0-1), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-4), gcc-13-base (= 13.3.0-4), gcc-13-x86-64-linux-gnu (= 13.3.0-4), gcc-14 (= 14.2.0-1), gcc-14-base (= 14.2.0-1), gcc-14-x86-64-linux-gnu (= 14.2.0-1), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-1), libatomic1 (= 14.2.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4+b1), libbinutils (= 2.42.90.20240720-2), libblkid1 (= 2.40.2-1), libbrotli-dev (= 1.1.0-2+b4), libbrotli1 (= 1.1.0-2+b4), libbz2-1.0 (= 1.0.8-5.1), libbz2-dev (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-1), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.90.20240720-2), libctf0 (= 2.42.90.20240720-2), libcurl3t64-gnutls (= 8.9.1-1), libcurl4-gnutls-dev (= 8.9.1-1), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdeflate-dev (= 1.20-1), libdeflate0 (= 1.20-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libevent-2.1-7t64 (= 2.1.12-stable-10), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-4), libgcc-14-dev (= 14.2.0-1), libgcc-s1 (= 14.2.0-1), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgmp-dev (= 2:6.3.0+dfsg-2+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgmpxx4ldbl (= 2:6.3.0+dfsg-2+b1), libgnutls-dane0t64 (= 3.8.6-2), libgnutls-openssl27t64 (= 3.8.6-2), libgnutls28-dev (= 3.8.6-2), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-1), libgprofng0 (= 2.42.90.20240720-2), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts-dev (= 1.20+ds-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.0-1+b1), libhwasan0 (= 14.2.0-1), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libidn2-dev (= 2.3.7-2), libio-pty-perl (= 1:1.20-1+b2), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-1), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), libldap-2.5-0 (= 2.5.18+dfsg-2+b1), liblsan0 (= 14.2.0-1), liblzma-dev (= 5.6.2-2), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncurses-dev (= 6.5-2), libncurses6 (= 6.5-2), libncursesw6 (= 6.5-2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.62.1-2), libnghttp2-dev (= 1.62.1-2), libnghttp3-9 (= 1.4.0-1), libnghttp3-dev (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls-dev (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libngtcp2-dev (= 1.6.0-1), libp11-kit-dev (= 0.25.5-2), libp11-kit0 (= 0.25.5-2), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libpkgconf3 (= 1.8.1-3), libpsl-dev (= 0.21.2-1.1), libpsl5t64 (= 0.21.2-1.1), libquadmath0 (= 14.2.0-1), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-6), libsasl2-modules-db (= 2.1.28+dfsg1-6), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b3), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libssh2-1-dev (= 1.11.0-7), libssh2-1t64 (= 1.11.0-7), libssl-dev (= 3.3.1-2), libssl3t64 (= 3.3.1-2), libstdc++-14-dev (= 14.2.0-1), libstdc++6 (= 14.2.0-1), libsystemd0 (= 256.4-2), libtasn1-6 (= 4.19.0-3+b2), libtasn1-6-dev (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-1), libubsan1 (= 14.2.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-2), libunbound8 (= 1.20.0-1+b1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-1), libxml2 (= 2.12.7+dfsg-3+b1), libzstd-dev (= 1.5.6+dfsg-1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.9.12-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240622-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), nettle-dev (= 3.10-1), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.09-2), tabix (= 1.20+ds-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.2-1), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1717095173" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ samtools-dbgsym_1.20-3_amd64.deb -------------------------------- new Debian package, version 2.0. size 991576 bytes: control archive=892 bytes. 619 bytes, 12 lines control 827 bytes, 8 lines md5sums Package: samtools-dbgsym Source: samtools Version: 1.20-3 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1062 Depends: samtools (= 1.20-3) Section: debug Priority: optional Description: debug symbols for samtools Build-Ids: 03af89567c606cee6e8b671ebce9c44b001edd1a 32abc2dd77ed20fd8a98345cd02122c2c6195c99 3dd375828b8cfe29a5ec0bcdbc21b8f5da4de266 46532afb2e553e06457a2df1e884a7a75687332f 757cdf787b4b4d0f5c3cb3691c544aaa5605d643 8da7e81e438ae4c0fa54e5695030af7258738290 9af7cb05cf434355039fb11aaf4feee016ad62ab drwxr-xr-x root/root 0 2024-05-30 18:52 ./ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/03/ -rw-r--r-- root/root 29496 2024-05-30 18:52 ./usr/lib/debug/.build-id/03/af89567c606cee6e8b671ebce9c44b001edd1a.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/32/ -rw-r--r-- root/root 7688 2024-05-30 18:52 ./usr/lib/debug/.build-id/32/abc2dd77ed20fd8a98345cd02122c2c6195c99.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/3d/ -rw-r--r-- root/root 11696 2024-05-30 18:52 ./usr/lib/debug/.build-id/3d/d375828b8cfe29a5ec0bcdbc21b8f5da4de266.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/46/ -rw-r--r-- root/root 22664 2024-05-30 18:52 ./usr/lib/debug/.build-id/46/532afb2e553e06457a2df1e884a7a75687332f.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/75/ -rw-r--r-- root/root 11680 2024-05-30 18:52 ./usr/lib/debug/.build-id/75/7cdf787b4b4d0f5c3cb3691c544aaa5605d643.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/8d/ -rw-r--r-- root/root 966232 2024-05-30 18:52 ./usr/lib/debug/.build-id/8d/a7e81e438ae4c0fa54e5695030af7258738290.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.build-id/9a/ -rw-r--r-- root/root 11544 2024-05-30 18:52 ./usr/lib/debug/.build-id/9a/f7cb05cf434355039fb11aaf4feee016ad62ab.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 3896 2024-05-30 18:52 ./usr/lib/debug/.dwz/x86_64-linux-gnu/samtools.debug drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-05-30 18:52 ./usr/share/doc/samtools-dbgsym -> samtools samtools-test_1.20-3_all.deb ---------------------------- new Debian package, version 2.0. size 2364248 bytes: control archive=16136 bytes. 516 bytes, 16 lines control 62178 bytes, 734 lines md5sums Package: samtools-test Source: samtools Version: 1.20-3 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 17342 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 2024-05-30 18:52 ./ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/doc/samtools-test/ -rw-r--r-- root/root 2198 2024-05-30 18:52 ./usr/share/doc/samtools-test/changelog.Debian.gz -rw-r--r-- root/root 36595 2024-04-15 14:10 ./usr/share/doc/samtools-test/changelog.gz -rw-r--r-- root/root 2250 2024-05-29 13:04 ./usr/share/doc/samtools-test/copyright drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/doc/samtools/ -rw-r--r-- root/root 364 2023-12-15 15:06 ./usr/share/doc/samtools/run-unit-test drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/ drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/ -rw-r--r-- root/root 1707 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/1_fixup.sam -rw-r--r-- root/root 1923 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/1_fixup.sam.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/1_fixup.sam.expected.err -rw-r--r-- root/root 1707 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam -rw-r--r-- root/root 1923 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected.err -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/3_fixup.sam.expected -rw-r--r-- root/root 79 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/3_fixup.sam.expected.err -rw-r--r-- root/root 1690 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam -rw-r--r-- root/root 1906 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected.err -rw-r--r-- root/root 1939 2024-04-15 14:10 ./usr/share/samtools/test/addrprg/5_editrg.sam.expected drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/ -rw-r--r-- root/root 4288 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_delete_tag.expected.sam -rw-r--r-- root/root 4408 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_fail.expected.sam -rw-r--r-- root/root 1663 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_filter.expected.sam -rw-r--r-- root/root 3933 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_hard_clipped.expected.sam -rw-r--r-- root/root 4611 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_original_tag.expected.sam -rw-r--r-- root/root 4405 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_soft_clipped.expected.sam -rw-r--r-- root/root 4405 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_soft_clipped_strand.expected.sam -rw-r--r-- root/root 4392 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/1_test_data.sam -rw-r--r-- root/root 2071 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/2_both_clipped.expected.sam -rw-r--r-- root/root 2075 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/2_both_test_data.sam -rw-r--r-- root/root 9276 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/3_multi_ref_both_clip.expected.sam -rw-r--r-- root/root 9270 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/3_multi_ref_clip.expected.sam -rw-r--r-- root/root 9229 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/3_multi_ref_data.sam -rw-r--r-- root/root 572 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/4_total_hc_data.expected.sam -rw-r--r-- root/root 1016 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/4_total_hc_data.sam -rw-r--r-- root/root 124 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/ac_test.bed -rw-r--r-- root/root 30 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/ac_test2.bed -rw-r--r-- root/root 348 2024-04-15 14:10 ./usr/share/samtools/test/ampliconclip/multi_ref.bed drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/ampliconstats/ -rw-r--r-- root/root 9352 2024-04-15 14:10 ./usr/share/samtools/test/ampliconstats/mixed_clipped.sam -rw-r--r-- root/root 10637 2024-04-15 14:10 ./usr/share/samtools/test/ampliconstats/stats.expected.txt -rw-r--r-- root/root 5188 2024-04-15 14:10 ./usr/share/samtools/test/ampliconstats/stats_mixed.expected.txt -rw-r--r-- root/root 3708 2024-04-15 14:10 ./usr/share/samtools/test/ampliconstats/stats_partial.expected.txt drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/ -rw-r--r-- root/root 767 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/1.1.fq.expected -rw-r--r-- root/root 767 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/1.2.fq.expected -rw-r--r-- root/root 712 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/10.1.fq.expected -rw-r--r-- root/root 712 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/10.2.fq.expected -rw-r--r-- root/root 96 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/10.s.fq.expected -rw-r--r-- root/root 1098 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/11.fa.expected -rw-r--r-- root/root 1606 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/11.fq.expected -rw-r--r-- root/root 864 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/12.1.fq.expected -rw-r--r-- root/root 864 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/12.2.fq.expected -rw-r--r-- root/root 116 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/12.i.fq.expected -rw-r--r-- root/root 112 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/12.s.fq.expected -rw-r--r-- root/root 219 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/13.fq.expected -rw-r--r-- root/root 53 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/14.0.fq.expected -rw-r--r-- root/root 25 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/14.i1.fq.expected -rw-r--r-- root/root 25 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/14.i2.fq.expected -rw-r--r-- root/root 3094 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/15.fq.expected -rw-r--r-- root/root 2280 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/16.fq.expected -rw-r--r-- root/root 2647 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/17.fq.expected -rw-r--r-- root/root 474 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/18.fq.expected -rw-r--r-- root/root 250 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/19.fq.expected -rw-r--r-- root/root 767 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/2.1.fq.expected -rw-r--r-- root/root 767 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/2.2.fq.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/2.s.fq.expected -rw-r--r-- root/root 156 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/20.fq.expected -rw-r--r-- root/root 767 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/3.1.fq.expected -rw-r--r-- root/root 767 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/3.2.fq.expected -rw-r--r-- root/root 41 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/3.s.fq.expected -rw-r--r-- root/root 712 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/4.1.fq.expected -rw-r--r-- root/root 712 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/4.2.fq.expected -rw-r--r-- root/root 96 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/4.s.fq.expected -rw-r--r-- root/root 746 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/5.1.fq.expected -rw-r--r-- root/root 746 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/5.2.fq.expected -rw-r--r-- root/root 100 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/5.s.fq.expected -rw-r--r-- root/root 964 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/6.1.fq.expected -rw-r--r-- root/root 916 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/6.2.fq.expected -rw-r--r-- root/root 120 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/6.s.fq.expected -rw-r--r-- root/root 1198 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/7.1.fq.expected -rw-r--r-- root/root 1104 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/7.2.fq.expected -rw-r--r-- root/root 128 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/7.s.fq.expected -rw-r--r-- root/root 861 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/8.1.fq.expected -rw-r--r-- root/root 861 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/8.2.fq.expected -rw-r--r-- root/root 109 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/8.i.fq.expected -rw-r--r-- root/root 112 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/8.s.fq.expected -rw-r--r-- root/root 1669 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/9.1.fq.expected -rw-r--r-- root/root 717 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/9.2.fq.expected -rw-r--r-- root/root 72 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/bc.fq.expected -rw-r--r-- root/root 72 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/bc10.fq.expected -rw-r--r-- root/root 82 2024-04-15 14:10 ./usr/share/samtools/test/bam2fq/bc_split.fq.expected drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/ -rw-r--r-- root/root 6152 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov.bam -rw-r--r-- root/root 7608 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov.bam.bai -rw-r--r-- root/root 23 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov.bed -rw-r--r-- root/root 26 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov.expected -rw-r--r-- root/root 31 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov_c.expected -rw-r--r-- root/root 23 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov_gG.bed -rw-r--r-- root/root 28 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov_gG.expected -rw-r--r-- root/root 25 2024-04-15 14:10 ./usr/share/samtools/test/bedcov/bedcov_j.expected drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/collate/ -rw-r--r-- root/root 12246 2024-04-15 14:10 ./usr/share/samtools/test/collate/1_fast_collate.sam.expected -rw-r--r-- root/root 12246 2024-04-15 14:10 ./usr/share/samtools/test/collate/2_fast_collate_with_tmp_used.sam.expected -rw-r--r-- root/root 1440 2024-04-15 14:10 ./usr/share/samtools/test/collate/collate.expected.sam -rw-r--r-- root/root 14085 2024-04-15 14:10 ./usr/share/samtools/test/collate/fast_collate.sam drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/consensus/ -rw-r--r-- root/root 494 2024-04-15 14:10 ./usr/share/samtools/test/consensus/consen1.sam -rw-r--r-- root/root 147 2024-04-15 14:10 ./usr/share/samtools/test/consensus/consen2.sam -rw-r--r-- root/root 750 2024-04-15 14:10 ./usr/share/samtools/test/consensus/consen3.sam -rw-r--r-- root/root 7403 2024-04-15 14:10 ./usr/share/samtools/test/consensus/consensus.reg drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/ -rw-r--r-- root/root 21 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/1.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/10.1q.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/10q.out -rw-r--r-- root/root 453 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/11.3p.out -rw-r--r-- root/root 42 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/11.3q.out -rw-r--r-- root/root 429 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/11.6p.out -rw-r--r-- root/root 42 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/11.6q.out -rw-r--r-- root/root 312 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/12p.out -rw-r--r-- root/root 56 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/12q.out -rw-r--r-- root/root 644 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/13p.out -rw-r--r-- root/root 86 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/13q.out -rw-r--r-- root/root 34 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/14p.out -rw-r--r-- root/root 12 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/14q.out -rw-r--r-- root/root 36 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/15p.out -rw-r--r-- root/root 220 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/16p.out -rw-r--r-- root/root 32 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/16q.out -rw-r--r-- root/root 94 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/17q.out -rw-r--r-- root/root 412 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/18p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/18q.out -rw-r--r-- root/root 411 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/19p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/19q.out -rw-r--r-- root/root 426 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/1p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/1q.out -rw-r--r-- root/root 22 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/2.out -rw-r--r-- root/root 417 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/20p.out -rw-r--r-- root/root 411 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/21p.out -rw-r--r-- root/root 426 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/22p.out -rw-r--r-- root/root 387 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/23p.out -rw-r--r-- root/root 370 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/24p.out -rw-r--r-- root/root 426 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/25p.out -rw-r--r-- root/root 426 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/26p.out -rw-r--r-- root/root 412 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/2p.out -rw-r--r-- root/root 42 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/2q.out -rw-r--r-- root/root 15 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/3.out -rw-r--r-- root/root 28 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/3q.out -rw-r--r-- root/root 16 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/4.out -rw-r--r-- root/root 412 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/4p.out -rw-r--r-- root/root 30 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/4q.out -rw-r--r-- root/root 419 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/5p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/5q.out -rw-r--r-- root/root 432 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/6p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/6q.out -rw-r--r-- root/root 432 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/7p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/7q.out -rw-r--r-- root/root 433 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/8p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/8q.out -rw-r--r-- root/root 419 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/9.1p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/9.1q.out -rw-r--r-- root/root 420 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/9p.out -rw-r--r-- root/root 40 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/9q.out -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/consensus/expected/empty.out drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/cram_size/ -rw-r--r-- root/root 439 2024-04-15 14:10 ./usr/share/samtools/test/cram_size/cram_size.reg drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/cram_size/expected/ -rw-r--r-- root/root 4973 2024-04-15 14:10 ./usr/share/samtools/test/cram_size/expected/encodings.out -rw-r--r-- root/root 2133 2024-04-15 14:10 ./usr/share/samtools/test/cram_size/expected/normal.out -rw-r--r-- root/root 3150 2024-04-15 14:10 ./usr/share/samtools/test/cram_size/expected/verbose.out -rw-r--r-- root/root 60965 2024-04-15 14:10 ./usr/share/samtools/test/cram_size/mpileup.1.cram drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/dat/ -rw-r--r-- root/root 5471 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.001.sam -rw-r--r-- root/root 5573 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.002.sam -rw-r--r-- root/root 5493 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.003.sam -rw-r--r-- root/root 5503 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.004.sam -rw-r--r-- root/root 5508 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.005.sam -rw-r--r-- root/root 5535 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.010.sam -rw-r--r-- root/root 1594 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.013.sam -rw-r--r-- root/root 112 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.014.sam -rw-r--r-- root/root 9707 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.703.sam -rw-r--r-- root/root 37 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.MD-D -rw-r--r-- root/root 6 2024-04-15 14:10 ./usr/share/samtools/test/dat/bam2fq.NM-D -rw-r--r-- root/root 1292 2024-04-15 14:10 ./usr/share/samtools/test/dat/cat.hdr drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/dat/cram_md5/ -rw-r--r-- root/root 57 2024-04-15 14:10 ./usr/share/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 -rw-r--r-- root/root 61 2024-04-15 14:10 ./usr/share/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 -rw-r--r-- root/root 36 2024-04-15 14:10 ./usr/share/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 -rw-r--r-- root/root 31 2024-04-15 14:10 ./usr/share/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b -rw-r--r-- root/root 42 2024-04-15 14:10 ./usr/share/samtools/test/dat/depad.001.fa -rw-r--r-- root/root 16 2024-04-15 14:10 ./usr/share/samtools/test/dat/depad.001.fa.fai -rw-r--r-- root/root 7964 2024-04-15 14:10 ./usr/share/samtools/test/dat/depad.001p.sam -rw-r--r-- root/root 7998 2024-04-15 14:10 ./usr/share/samtools/test/dat/depad.001u.sam -rw-r--r-- root/root 135 2024-04-15 14:10 ./usr/share/samtools/test/dat/dict.alias.fa -rw-r--r-- root/root 618 2024-04-15 14:10 ./usr/share/samtools/test/dat/dict.alias.out -rw-r--r-- root/root 46 2024-04-15 14:10 ./usr/share/samtools/test/dat/dict.alt -rw-r--r-- root/root 525 2024-04-15 14:10 ./usr/share/samtools/test/dat/dict.alt.out -rw-r--r-- root/root 2300 2024-04-15 14:10 ./usr/share/samtools/test/dat/dict.fa -rw-r--r-- root/root 1484 2024-04-15 14:10 ./usr/share/samtools/test/dat/dict.out -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/dat/empty.expected -rw-r--r-- root/root 624 2024-04-15 14:10 ./usr/share/samtools/test/dat/large_chrom.out -rw-r--r-- root/root 5090 2024-04-15 14:10 ./usr/share/samtools/test/dat/large_chrom.sam -rw-r--r-- root/root 92 2024-04-15 14:10 ./usr/share/samtools/test/dat/large_chrom_bai_index.err -rw-r--r-- root/root 350835 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.1.sam -rw-r--r-- root/root 104818 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.2.sam -rw-r--r-- root/root 105780 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.3.sam -rw-r--r-- root/root 37 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.err.1 -rw-r--r-- root/root 2715 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.out.1 -rw-r--r-- root/root 81714 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.out.2 -rw-r--r-- root/root 295 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.out.3 -rw-r--r-- root/root 113952 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.out.4 -rw-r--r-- root/root 23 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.out.5 -rw-r--r-- root/root 4284 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.ref.fa -rw-r--r-- root/root 17 2024-04-15 14:10 ./usr/share/samtools/test/dat/mpileup.ref.fa.fai -rw-r--r-- root/root 819 2024-04-15 14:10 ./usr/share/samtools/test/dat/sort_name_input_1.sam -rw-r--r-- root/root 759 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_a.bam -rw-r--r-- root/root 264 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_a.bam.bai.expected -rw-r--r-- root/root 3178 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_a.cram -rw-r--r-- root/root 1429 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_a.sam -rw-r--r-- root/root 1576 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_a_regex.sam -rw-r--r-- root/root 1349 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_ab.X.expected -rw-r--r-- root/root 545 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_b.X.expected -rw-r--r-- root/root 1014 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_b.X2.expected -rw-r--r-- root/root 686 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_b.bam -rw-r--r-- root/root 1252 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_b.sam -rw-r--r-- root/root 1369 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_b_regex.sam -rw-r--r-- root/root 692 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_c.bam -rw-r--r-- root/root 1293 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_c.sam -rw-r--r-- root/root 1419 2024-04-15 14:10 ./usr/share/samtools/test/dat/test_input_1_d.sam -rw-r--r-- root/root 1335 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.001.01.bed -rw-r--r-- root/root 1134 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.001.02.bed -rw-r--r-- root/root 1349 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.001.03.bed -rw-r--r-- root/root 214 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.001.fa -rw-r--r-- root/root 58 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.001.fa.fai -rw-r--r-- root/root 5121 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.001.sam -rw-r--r-- root/root 1313 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.002.01.bed -rw-r--r-- root/root 1302 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.002.02.bed -rw-r--r-- root/root 64 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.002.fa -rw-r--r-- root/root 13 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.002.fa.fai -rw-r--r-- root/root 3692 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.002.sam -rw-r--r-- root/root 2142 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.003.expected.sam -rw-r--r-- root/root 2224 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.003.sam -rw-r--r-- root/root 5158 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.004.expected.sam -rw-r--r-- root/root 4052 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.005.expected.sam -rw-r--r-- root/root 4392 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.005.sam -rw-r--r-- root/root 4322 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.005.unmap.expected.sam -rw-r--r-- root/root 7305 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.fetch-pairs.bam -rw-r--r-- root/root 16244 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.fetch-pairs.expected.sam -rw-r--r-- root/root 19278 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.fetch-pairs.filter0.expected.sam -rw-r--r-- root/root 16241 2024-04-15 14:10 ./usr/share/samtools/test/dat/view.fetch-pairs.filter1.expected.sam drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/ -rw-r--r-- root/root 965 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/1_coord_sort.sam -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected -rw-r--r-- root/root 82 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected.err -rw-r--r-- root/root 1118 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam -rw-r--r-- root/root 1260 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam.expected -rw-r--r-- root/root 715 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam -rw-r--r-- root/root 733 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected -rw-r--r-- root/root 715 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam -rw-r--r-- root/root 733 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected -rw-r--r-- root/root 715 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/5_ct.sam -rw-r--r-- root/root 753 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/5_ct.sam.expected -rw-r--r-- root/root 735 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/6_ct_replace.sam -rw-r--r-- root/root 753 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/6_ct_replace.sam.expected -rw-r--r-- root/root 1191 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/7_two_read_mapped.sam -rw-r--r-- root/root 1334 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/7_two_read_mapped.sam.expected -rw-r--r-- root/root 1327 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/8_isize_overflow_64bit.sam -rw-r--r-- root/root 1508 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/8_isize_overflow_64bit.sam.expected -rw-r--r-- root/root 436 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ML_only.sam -rw-r--r-- root/root 369 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ML_only.sam.expected -rw-r--r-- root/root 458 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ML_wrong_len.sam -rw-r--r-- root/root 360 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ML_wrong_len.sam.expected -rw-r--r-- root/root 400 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_MN_only.sam -rw-r--r-- root/root 369 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_MN_only.sam.expected -rw-r--r-- root/root 561 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_bad_MN.sam -rw-r--r-- root/root 561 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_bad_MN.sam.expected -rw-r--r-- root/root 280 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_bounds.sam -rw-r--r-- root/root 244 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_bounds.sam.expected -rw-r--r-- root/root 549 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_draft.sam -rw-r--r-- root/root 549 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_draft.sam.expected -rw-r--r-- root/root 441 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_noseq.sam -rw-r--r-- root/root 369 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_noseq.sam.expected -rw-r--r-- root/root 1042 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_not_updated.sam -rw-r--r-- root/root 922 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_not_updated.sam.expected -rw-r--r-- root/root 866 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_not_updated_noML.sam -rw-r--r-- root/root 815 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_not_updated_noML.sam.expected -rw-r--r-- root/root 978 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_not_updated_noMN.sam -rw-r--r-- root/root 922 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_not_updated_noMN.sam.expected -rw-r--r-- root/root 890 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_not_updated_noseq.sam -rw-r--r-- root/root 549 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ok+.sam -rw-r--r-- root/root 549 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ok+.sam.expected -rw-r--r-- root/root 550 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ok-.sam -rw-r--r-- root/root 550 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/mod_ok-.sam.expected -rw-r--r-- root/root 2884 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/sanitize.sam -rw-r--r-- root/root 2818 2024-04-15 14:10 ./usr/share/samtools/test/fixmate/sanitize.sam.expected drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/idxstats/ -rw-r--r-- root/root 58 2024-04-15 14:10 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected.err drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/import/ -rw-r--r-- root/root 2518 2024-04-15 14:10 ./usr/share/samtools/test/import/1.expected.sam -rw-r--r-- root/root 1705 2024-04-15 14:10 ./usr/share/samtools/test/import/2.expected.sam -rw-r--r-- root/root 1320 2024-04-15 14:10 ./usr/share/samtools/test/import/2.interleaved.fq -rw-r--r-- root/root 1344 2024-04-15 14:10 ./usr/share/samtools/test/import/3.interleaved.fq -rw-r--r-- root/root 286 2024-04-15 14:10 ./usr/share/samtools/test/import/4.aux.fq -rw-r--r-- root/root 342 2024-04-15 14:10 ./usr/share/samtools/test/import/4.expected-XZ,XA,AA.sam -rw-r--r-- root/root 414 2024-04-15 14:10 ./usr/share/samtools/test/import/4.expected.sam -rw-r--r-- root/root 382 2024-04-15 14:10 ./usr/share/samtools/test/import/5-BC.expected.sam -rw-r--r-- root/root 382 2024-04-15 14:10 ./usr/share/samtools/test/import/5-OX.expected.sam -rw-r--r-- root/root 26 2024-04-15 14:10 ./usr/share/samtools/test/import/5-i1.fq -rw-r--r-- root/root 34 2024-04-15 14:10 ./usr/share/samtools/test/import/5-i2.fq -rw-r--r-- root/root 66 2024-04-15 14:10 ./usr/share/samtools/test/import/5-r1.fq -rw-r--r-- root/root 66 2024-04-15 14:10 ./usr/share/samtools/test/import/5-r2.fq drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/ -rw-r--r-- root/root 6292 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/depth.expected.out -rw-r--r-- root/root 82 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/depth_bed.expected.out -rw-r--r-- root/root 31742 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/longref.sam -rw-r--r-- root/root 28433 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/longref2.sam -rw-r--r-- root/root 4740 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/longref3.expected.sam -rw-r--r-- root/root 2947 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/longref3.sam -rw-r--r-- root/root 6721 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/longref_idx.expected.sam -rw-r--r-- root/root 31741 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/longref_name.sam -rw-r--r-- root/root 60115 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/merge.expected.sam -rw-r--r-- root/root 37 2024-04-15 14:10 ./usr/share/samtools/test/large_pos/test.bed -rw-r--r-- root/root 3888 2024-04-15 14:10 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./usr/share/samtools/test/mpileup/expected/a14.out -rw-r--r-- root/root 483 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a15.out -rw-r--r-- root/root 483 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a16.out -rw-r--r-- root/root 563 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a17.out -rw-r--r-- root/root 277 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a2.out -rw-r--r-- root/root 403 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a3.out -rw-r--r-- root/root 819 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a4.out -rw-r--r-- root/root 819 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a5.out -rw-r--r-- root/root 1185 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a6.out -rw-r--r-- root/root 247 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a8.out -rw-r--r-- root/root 247 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/a9.out -rw-r--r-- root/root 5 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/csize.out -rw-r--r-- root/root 45 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d1_1.out -rw-r--r-- root/root 86 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d1_12.out -rw-r--r-- root/root 45 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d1_2.out -rw-r--r-- root/root 48 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d2_12r.out -rw-r--r-- root/root 191 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d3_12.out -rw-r--r-- root/root 115 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d3_12r1a.out -rw-r--r-- root/root 58 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d3_12r2a.out -rw-r--r-- root/root 302 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d3_3.out -rw-r--r-- root/root 573 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d4_12.out -rw-r--r-- root/root 165 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d4_12b.out -rw-r--r-- root/root 115 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d4_12r.out -rw-r--r-- root/root 45 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_all1.out -rw-r--r-- root/root 302 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_all2.out -rw-r--r-- root/root 604 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_all3.out -rw-r--r-- root/root 453 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_all4.out -rw-r--r-- root/root 21 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_b3.out -rw-r--r-- root/root 50 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_b3a.out -rw-r--r-- root/root 104 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_b3aa.out -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_blank.out -rw-r--r-- root/root 21 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_xx1.out -rw-r--r-- root/root 50 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_xx2.out -rw-r--r-- root/root 95 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_xx3.out -rw-r--r-- root/root 14 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d5_xy1.out -rw-r--r-- root/root 252 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d6_nodel.out -rw-r--r-- root/root 252 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d6_wdel.out -rw-r--r-- root/root 487 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d7_nodup.out -rw-r--r-- root/root 375 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d8_PROPER.out -rw-r--r-- root/root 455 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d8_PROSUP.out -rw-r--r-- root/root 487 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d8_QC.out -rw-r--r-- root/root 231 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d8_R1PROP.out -rw-r--r-- root/root 487 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d8_noQC.out -rw-r--r-- root/root 455 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/d8_noSUPP.out -rw-r--r-- root/root 87 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_all1.out -rw-r--r-- root/root 548 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_all2.out -rw-r--r-- root/root 1090 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_all3.out -rw-r--r-- root/root 42 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_b3.out -rw-r--r-- root/root 95 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_b3a.out -rw-r--r-- root/root 191 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_b3aa.out -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_blank.out -rw-r--r-- root/root 42 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_xx1.out -rw-r--r-- root/root 95 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_xx2.out -rw-r--r-- root/root 167 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_xx3.out -rw-r--r-- root/root 26 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/m5_xy1.out -rw-r--r-- root/root 163207 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp1_d.out -rw-r--r-- root/root 163199 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp1_dd.out -rw-r--r-- root/root 161728 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp1_ends.out -rw-r--r-- root/root 163203 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp1_i.out -rw-r--r-- root/root 163187 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp1_ii.out -rw-r--r-- root/root 163175 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp1_iidd.out -rw-r--r-- root/root 870 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp2-noins.out -rw-r--r-- root/root 876 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp2.out -rw-r--r-- root/root 248 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_2018a.out -rw-r--r-- root/root 490 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_2018aa.out -rw-r--r-- root/root 197 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_D.out -rw-r--r-- root/root 275 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_DI.out -rw-r--r-- root/root 197 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_I.out -rw-r--r-- root/root 259 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_ID.out -rw-r--r-- root/root 259 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_ID_rev.out -rw-r--r-- root/root 188 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_N.out -rw-r--r-- root/root 377 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_N2.out -rw-r--r-- root/root 241 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/expected/mp_P.out -rw-r--r-- root/root 1561 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/indels.sam drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/md5/ -rw-r--r-- root/root 200 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae -rw-r--r-- root/root 200 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d -rw-r--r-- root/root 4200 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de -rw-r--r-- root/root 200 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc -rw-r--r-- root/root 200 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 -rw-r--r-- root/root 200 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e -rw-r--r-- root/root 757 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mod1.sam -rw-r--r-- root/root 17 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp.fa -rw-r--r-- root/root 13 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp.fa.fai -rw-r--r-- root/root 56 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_2018.fa -rw-r--r-- root/root 55 2024-05-30 18:52 ./usr/share/samtools/test/mpileup/mp_2018.fa.fai -rw-r--r-- root/root 124 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_2018.sam -rw-r--r-- root/root 295 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_D.sam -rw-r--r-- root/root 429 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_DI.sam -rw-r--r-- root/root 504 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_I.sam -rw-r--r-- root/root 416 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_ID.sam -rw-r--r-- root/root 421 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_ID_rev.sam -rw-r--r-- root/root 295 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_N.sam -rw-r--r-- root/root 484 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_N2.sam -rw-r--r-- root/root 432 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mp_P.sam -rw-r--r-- root/root 280 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup-E.bam -rw-r--r-- root/root 71637 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup.1.bam -rw-r--r-- root/root 776 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup.1.bam.bai -rw-r--r-- root/root 31556 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup.2.bam -rw-r--r-- root/root 31216 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup.3.bam -rw-r--r-- root/root 4284 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup.ref.fa -rw-r--r-- root/root 17 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup.ref.fa.fai -rw-r--r-- root/root 9132 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/mpileup.reg -rw-r--r-- root/root 210 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/output-BP.sam -rw-r--r-- root/root 376 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/overlap.bam -rw-r--r-- root/root 793 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/overlap50.sam -rw-r--r-- root/root 583 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/overlapIllumina.bam -rw-r--r-- root/root 250 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/regions -rw-r--r-- root/root 279 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx#depth1.sam -rw-r--r-- root/root 279 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx#depth2.sam -rw-r--r-- root/root 346 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx#depth3.sam -rw-r--r-- root/root 521 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx#depth4.sam -rw-r--r-- root/root 215 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx#minimal.bam -rw-r--r-- root/root 247 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx#triplet.bam -rw-r--r-- root/root 17 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx.bed -rw-r--r-- root/root 8 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx.bed2 -rw-r--r-- root/root 24 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx.bed3 -rw-r--r-- root/root 55 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx.fa -rw-r--r-- root/root 29 2024-04-15 14:10 ./usr/share/samtools/test/mpileup/xx.fa.fai drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/ -rw-r--r-- root/root 1228 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/1.quickcheck.badeof.bam -rw-r--r-- root/root 500 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/10.quickcheck.notargets.bam -rw-r--r-- root/root 1233 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/2.quickcheck.badheader.bam -rw-r--r-- root/root 1228 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/3.quickcheck.ok.bam -rw-r--r-- root/root 1233 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/4.quickcheck.ok.bam -rw-r--r-- root/root 11960 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/5.quickcheck.scramble30.truncated.cram -rw-r--r-- root/root 154443 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/6.quickcheck.cram21.ok.cram -rw-r--r-- root/root 49122 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/7.quickcheck.cram30.ok.cram -rw-r--r-- root/root 154413 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/8.quickcheck.cram21.truncated.cram -rw-r--r-- root/root 49084 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/9.quickcheck.cram30.truncated.cram -rw-r--r-- root/root 188 2024-04-15 14:10 ./usr/share/samtools/test/quickcheck/all.expected drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/reference/ -rw-r--r-- root/root 4274 2024-04-15 14:10 ./usr/share/samtools/test/reference/mpileup.MD.fa.expected -rw-r--r-- root/root 4274 2024-04-15 14:10 ./usr/share/samtools/test/reference/mpileup.embed.fa.expected -rwxr-xr-x root/root 4969 2024-04-15 14:10 ./usr/share/samtools/test/regression.sh drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/reheader/ -rw-r--r-- root/root 5079 2024-04-15 14:10 ./usr/share/samtools/test/reheader/1_view1.sam.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/reheader/1_view1.sam.expected.err -rw-r--r-- root/root 5079 2024-04-15 14:10 ./usr/share/samtools/test/reheader/2_view1.sam.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/reheader/2_view1.sam.expected.err -rw-r--r-- root/root 5079 2024-04-15 14:10 ./usr/share/samtools/test/reheader/3_view1.sam.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/reheader/3_view1.sam.expected.err -rw-r--r-- root/root 5127 2024-04-15 14:10 ./usr/share/samtools/test/reheader/4_view1.sam.expected -rw-r--r-- root/root 5121 2024-04-15 14:10 ./usr/share/samtools/test/reheader/5_view1.sam.expected -rw-r--r-- root/root 1477 2024-04-15 14:10 ./usr/share/samtools/test/reheader/hdr.sam drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/reset/ -rw-r--r-- root/root 241116 2024-04-15 14:10 ./usr/share/samtools/test/reset/basic.1.mp.1.expected -rw-r--r-- root/root 1128 2024-04-15 14:10 ./usr/share/samtools/test/reset/basic.bam.input.expected -rw-r--r-- root/root 1128 2024-04-15 14:10 ./usr/share/samtools/test/reset/basic.cram.input.expected -rw-r--r-- root/root 347059 2024-04-15 14:10 ./usr/share/samtools/test/reset/basic.output.mp.1.expected -rw-r--r-- root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/reset/empty.expected -rw-r--r-- root/root 129 2024-04-15 14:10 ./usr/share/samtools/test/reset/output.flg.1.expected -rw-r--r-- root/root 146152 2024-04-15 14:10 ./usr/share/samtools/test/reset/output.keep.1.expected -rw-r--r-- root/root 219161 2024-04-15 14:10 ./usr/share/samtools/test/reset/output.keep.2.expected -rw-r--r-- root/root 149995 2024-04-15 14:10 ./usr/share/samtools/test/reset/output.keep.3.expected -rw-r--r-- root/root 232581 2024-04-15 14:10 ./usr/share/samtools/test/reset/output.nRG.1.expected -rw-r--r-- root/root 136575 2024-04-15 14:10 ./usr/share/samtools/test/reset/output.nRG.2.expected -rw-r--r-- root/root 2 2024-04-15 14:10 ./usr/share/samtools/test/reset/reject.1.expected -rw-r--r-- root/root 3 2024-04-15 14:10 ./usr/share/samtools/test/reset/reject.2.expected -rw-r--r-- root/root 343 2024-04-15 14:10 ./usr/share/samtools/test/reset/seq.sam drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/sort/ -rw-r--r-- root/root 351072 2024-04-15 14:10 ./usr/share/samtools/test/sort/minimiser-basic.sam -rw-r--r-- root/root 373007 2024-04-15 14:10 ./usr/share/samtools/test/sort/minimiser-indexed-poly.sam -rw-r--r-- root/root 372968 2024-04-15 14:10 ./usr/share/samtools/test/sort/minimiser-indexed.sam -rw-r--r-- root/root 1463 2024-04-15 14:10 ./usr/share/samtools/test/sort/name.sort.expected.sam -rw-r--r-- root/root 1294 2024-04-15 14:10 ./usr/share/samtools/test/sort/name2.sort.expected.sam -rw-r--r-- root/root 944 2024-04-15 14:10 ./usr/share/samtools/test/sort/name3.sort.expected.sam -rw-r--r-- root/root 1443 2024-04-15 14:10 ./usr/share/samtools/test/sort/pos.sort.expected.sam -rw-r--r-- root/root 1430 2024-04-15 14:10 ./usr/share/samtools/test/sort/tag.as.sort.expected.sam -rw-r--r-- root/root 1430 2024-04-15 14:10 ./usr/share/samtools/test/sort/tag.fi.sort.expected.sam -rw-r--r-- root/root 1440 2024-04-15 14:10 ./usr/share/samtools/test/sort/tag.rg.n.sort.expected.sam -rw-r--r-- root/root 1440 2024-04-15 14:10 ./usr/share/samtools/test/sort/tag.rg.sort.expected.sam -rw-r--r-- root/root 3185 2024-04-15 14:10 ./usr/share/samtools/test/sort/template-coordinate.sort.expected.sam -rw-r--r-- root/root 3144 2024-04-15 14:10 ./usr/share/samtools/test/sort/template-coordinate.sort.sam drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/split/ -rw-r--r-- root/root 3169 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected.grp1.sam -rw-r--r-- root/root 2924 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected.grp2.sam -rw-r--r-- root/root 2085 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected.unk.sam -rw-r--r-- root/root 1628 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_RG.grp3.sam -rw-r--r-- root/root 1869 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_RG.unk.sam -rw-r--r-- root/root 1930 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_an.aardvark.sam -rw-r--r-- root/root 2870 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_an.badger.sam -rw-r--r-- root/root 2595 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_an.cat.sam -rw-r--r-- root/root 2076 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_an.dog.sam -rw-r--r-- root/root 1865 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_an.unk.sam -rw-r--r-- root/root 2303 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_an_M_3.unk.sam -rw-r--r-- root/root 1937 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_nn.-1.sam -rw-r--r-- root/root 2317 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_nn.-2.sam -rw-r--r-- root/root 2064 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_nn.1.sam -rw-r--r-- root/root 3153 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_nn.2.sam -rw-r--r-- root/root 2072 2024-04-15 14:10 ./usr/share/samtools/test/split/split.expected_d_nn.unk.sam -rw-r--r-- root/root 5368 2024-04-15 14:10 ./usr/share/samtools/test/split/split.sam -rw-r--r-- root/root 5575 2024-04-15 14:10 ./usr/share/samtools/test/split/split_d_nn.sam -rw-r--r-- root/root 3627 2024-04-15 14:10 ./usr/share/samtools/test/split/test_count_rg.c -rw-r--r-- root/root 6038 2024-04-15 14:10 ./usr/share/samtools/test/split/test_expand_format_string.c -rw-r--r-- root/root 9529 2024-04-15 14:10 ./usr/share/samtools/test/split/test_filter_header_rg.c -rw-r--r-- root/root 6828 2024-04-15 14:10 ./usr/share/samtools/test/split/test_parse_args.c drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/samtools/test/stat/ -rw-r--r-- root/root 66357 2024-04-15 14:10 ./usr/share/samtools/test/stat/1.stats.expected -rw-r--r-- root/root 47440 2024-04-15 14:10 ./usr/share/samtools/test/stat/1.stats.large.expected -rw-r--r-- root/root 66365 2024-04-15 14:10 ./usr/share/samtools/test/stat/10.stats.expected -rw-r--r-- root/root 433 2024-04-15 14:10 ./usr/share/samtools/test/stat/10_map_cigar.sam -rw-r--r-- root/root 66357 2024-04-15 14:10 ./usr/share/samtools/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat -rw-r--r-- root/root 66357 2024-04-15 14:10 ./usr/share/samtools/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat -rw-r--r-- root/root 8591 2024-04-15 14:10 ./usr/share/samtools/test/stat/11.stats.expected -rw-r--r-- root/root 8590 2024-04-15 14:10 ./usr/share/samtools/test/stat/11.stats.g4.expected -rw-r--r-- root/root 1162 2024-04-15 14:10 ./usr/share/samtools/test/stat/11.stats.targets -rw-r--r-- root/root 1937 2024-04-15 14:10 ./usr/share/samtools/test/stat/11_target.bam -rw-r--r-- root/root 192 2024-04-15 14:10 ./usr/share/samtools/test/stat/11_target.bam.bai -rw-r--r-- root/root 4546 2024-04-15 14:10 ./usr/share/samtools/test/stat/11_target.sam -rw-r--r-- root/root 42445 2024-04-15 14:10 ./usr/share/samtools/test/stat/12.2reads.nooverlap.expected -rw-r--r-- root/root 42460 2024-04-15 14:10 ./usr/share/samtools/test/stat/12.2reads.overlap.expected -rw-r--r-- root/root 41951 2024-04-15 14:10 ./usr/share/samtools/test/stat/12.3reads.nooverlap.expected -rw-r--r-- root/root 41965 2024-04-15 14:10 ./usr/share/samtools/test/stat/12.3reads.overlap.expected -rw-r--r-- root/root 21 2024-04-15 14:10 ./usr/share/samtools/test/stat/12_2reads.bed -rw-r--r-- root/root 21 2024-04-15 14:10 ./usr/share/samtools/test/stat/12_3reads.bed -rw-r--r-- root/root 1176 2024-04-15 14:10 ./usr/share/samtools/test/stat/12_overlaps.bam -rw-r--r-- root/root 11418 2024-04-15 14:10 ./usr/share/samtools/test/stat/13.barcodes.bc.ok.expected -rw-r--r-- root/root 13902 2024-04-15 14:10 ./usr/share/samtools/test/stat/13.barcodes.ox.ok.expected -rw-r--r-- root/root 330764 2024-04-15 14:10 ./usr/share/samtools/test/stat/13_barcodes_fail_bc_length.sam -rw-r--r-- root/root 330763 2024-04-15 14:10 ./usr/share/samtools/test/stat/13_barcodes_fail_hyphen.sam -rw-r--r-- root/root 330764 2024-04-15 14:10 ./usr/share/samtools/test/stat/13_barcodes_fail_qt_length.sam -rw-r--r-- root/root 330763 2024-04-15 14:10 ./usr/share/samtools/test/stat/13_barcodes_ok.sam -rw-r--r-- root/root 392771 2024-04-15 14:10 ./usr/share/samtools/test/stat/13_barcodes_ok_ox_bz.sam -rw-r--r-- root/root 8499 2024-04-15 14:10 ./usr/share/samtools/test/stat/14.rg.Sample.expected -rw-r--r-- root/root 8345 2024-04-15 14:10 ./usr/share/samtools/test/stat/14.rg.grp2.expected -rw-r--r-- root/root 4484 2024-04-15 14:10 ./usr/share/samtools/test/stat/14.rg.grp3.expected -rw-r--r-- root/root 47440 2024-04-15 14:10 ./usr/share/samtools/test/stat/14.rg.s1.expected -rw-r--r-- root/root 213 2024-04-15 14:10 ./usr/share/samtools/test/stat/15.big_del.sam -rw-r--r-- root/root 15335 2024-04-15 14:10 ./usr/share/samtools/test/stat/15.stats.expected -rw-r--r-- root/root 232 2024-04-15 14:10 ./usr/share/samtools/test/stat/1_map_cigar.sam -rw-r--r-- root/root 66357 2024-04-15 14:10 ./usr/share/samtools/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat -rw-r--r-- root/root 278 2024-04-15 14:10 ./usr/share/samtools/test/stat/1_map_cigar_large.sam -rw-r--r-- root/root 66357 2024-04-15 14:10 ./usr/share/samtools/test/stat/2.stats.expected -rw-r--r-- root/root 47440 2024-04-15 14:10 ./usr/share/samtools/test/stat/2.stats.large.expected -rw-r--r-- root/root 232 2024-04-15 14:10 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq.sam -rw-r--r-- root/root 278 2024-04-15 14:10 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq_large.sam -rw-r--r-- root/root 61254 2024-04-15 14:10 ./usr/share/samtools/test/stat/3.stats.expected -rw-r--r-- root/root 42337 2024-04-15 14:10 ./usr/share/samtools/test/stat/3.stats.large.expected -rw-r--r-- root/root 232 2024-04-15 14:10 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq.sam -rw-r--r-- root/root 278 2024-04-15 14:10 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq_large.sam -rw-r--r-- root/root 66357 2024-04-15 14:10 ./usr/share/samtools/test/stat/4.stats.expected -rw-r--r-- root/root 47440 2024-04-15 14:10 ./usr/share/samtools/test/stat/4.stats.large.expected -rw-r--r-- root/root 234 2024-04-15 14:10 ./usr/share/samtools/test/stat/4_X_cigar_full_seq.sam -rw-r--r-- root/root 280 2024-04-15 14:10 ./usr/share/samtools/test/stat/4_X_cigar_full_seq_large.sam -rw-r--r-- root/root 66379 2024-04-15 14:10 ./usr/share/samtools/test/stat/5.stats.expected -rw-r--r-- root/root 47462 2024-04-15 14:10 ./usr/share/samtools/test/stat/5.stats.large.expected -rw-r--r-- root/root 236 2024-04-15 14:10 ./usr/share/samtools/test/stat/5_insert_cigar.sam -rw-r--r-- root/root 282 2024-04-15 14:10 ./usr/share/samtools/test/stat/5_insert_cigar_large.sam -rw-r--r-- root/root 66379 2024-04-15 14:10 ./usr/share/samtools/test/stat/6.stats.expected -rw-r--r-- root/root 66393 2024-04-15 14:10 ./usr/share/samtools/test/stat/7.stats.expected -rw-r--r-- root/root 47476 2024-04-15 14:10 ./usr/share/samtools/test/stat/7.stats.large.expected -rw-r--r-- root/root 301 2024-04-15 14:10 ./usr/share/samtools/test/stat/7_supp.sam -rw-r--r-- root/root 366 2024-04-15 14:10 ./usr/share/samtools/test/stat/7_supp_large.sam -rw-r--r-- root/root 66379 2024-04-15 14:10 ./usr/share/samtools/test/stat/8.stats.expected -rw-r--r-- root/root 47462 2024-04-15 14:10 ./usr/share/samtools/test/stat/8.stats.large.expected -rw-r--r-- root/root 328 2024-04-15 14:10 ./usr/share/samtools/test/stat/8_secondary.sam -rw-r--r-- root/root 393 2024-04-15 14:10 ./usr/share/samtools/test/stat/8_secondary_large.sam -rw-r--r-- root/root 66357 2024-04-15 14:10 ./usr/share/samtools/test/stat/9.stats.expected -rw-r--r-- root/root 109 2024-04-15 14:10 ./usr/share/samtools/test/stat/test.fa -rw-r--r-- root/root 18 2024-04-15 14:10 ./usr/share/samtools/test/stat/test.fa.fai -rw-r--r-- root/root 2803 2024-04-15 14:10 ./usr/share/samtools/test/test.c -rw-r--r-- root/root 1466 2024-04-15 14:10 ./usr/share/samtools/test/test.h -rwxr-xr-x root/root 179782 2024-05-30 18:52 ./usr/share/samtools/test/test.pl drwxr-xr-x root/root 0 2024-04-15 14:10 ./usr/share/samtools/test/tview/ -rw-r--r-- root/root 2445 2024-04-15 14:10 ./usr/share/samtools/test/tview/test_get_rg_sample.c -rw-r--r-- root/root 3401 2024-04-15 14:10 ./usr/share/samtools/test/vcf-miniview.c samtools_1.20-3_amd64.deb ------------------------- new Debian package, version 2.0. size 657552 bytes: control archive=2944 bytes. 836 bytes, 17 lines control 5675 bytes, 83 lines md5sums Package: samtools Version: 1.20-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1429 Depends: libc6 (>= 2.34), libhts3t64 (>= 1.20~), 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 2024-05-30 18:52 ./ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/bin/ -rwxr-xr-x root/root 26856 2024-05-30 18:52 ./usr/bin/ace2sam -rwxr-xr-x root/root 5443 2024-05-30 18:52 ./usr/bin/blast2sam.pl -rwxr-xr-x root/root 3360 2024-05-30 18:52 ./usr/bin/bowtie2sam.pl -rwxr-xr-x root/root 17996 2024-05-30 18:52 ./usr/bin/export2sam.pl -rwxr-xr-x root/root 3300 2024-05-30 18:52 ./usr/bin/fasta-sanitize.pl -rwxr-xr-x root/root 6121 2024-05-30 18:52 ./usr/bin/interpolate_sam.pl -rwxr-xr-x root/root 14568 2024-05-30 18:52 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 14568 2024-05-30 18:52 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 14568 2024-05-30 18:52 ./usr/bin/md5fa -rwxr-xr-x root/root 14568 2024-05-30 18:52 ./usr/bin/md5sum-lite -rwxr-xr-x root/root 7969 2024-05-30 18:52 ./usr/bin/novo2sam.pl -rwxr-xr-x root/root 44331 2024-05-30 18:52 ./usr/bin/plot-ampliconstats -rwxr-xr-x root/root 55298 2024-05-30 18:52 ./usr/bin/plot-bamstats -rwxr-xr-x root/root 3204 2024-05-30 18:52 ./usr/bin/psl2sam.pl -rwxr-xr-x root/root 8957 2024-05-30 18:52 ./usr/bin/sam2vcf.pl -rwxr-xr-x root/root 779632 2024-05-30 18:52 ./usr/bin/samtools -rwxr-xr-x root/root 16474 2024-05-30 18:52 ./usr/bin/samtools.pl -rwxr-xr-x root/root 11333 2024-05-30 18:52 ./usr/bin/seq_cache_populate.pl -rwxr-xr-x root/root 3905 2024-05-30 18:52 ./usr/bin/soap2sam.pl -rwxr-xr-x root/root 22800 2024-05-30 18:52 ./usr/bin/wgsim -rwxr-xr-x root/root 12542 2024-05-30 18:52 ./usr/bin/wgsim_eval.pl -rwxr-xr-x root/root 3579 2024-05-30 18:52 ./usr/bin/zoom2sam.pl drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/commonwl/ -rwxr-xr-x root/root 1906 2023-12-15 15:06 ./usr/share/commonwl/samtools-faidx.cwl -rwxr-xr-x root/root 1979 2023-12-15 15:06 ./usr/share/commonwl/samtools-index.cwl -rwxr-xr-x root/root 1627 2023-12-15 15:06 ./usr/share/commonwl/samtools-rmdup.cwl -rwxr-xr-x root/root 2834 2023-12-15 15:06 ./usr/share/commonwl/samtools-sort.cwl -rwxr-xr-x root/root 6224 2023-12-15 15:06 ./usr/share/commonwl/samtools-view.cwl drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/doc/samtools/ -rw-r--r-- root/root 828 2024-04-15 14:10 ./usr/share/doc/samtools/AUTHORS -rw-r--r-- root/root 497 2023-12-15 15:06 ./usr/share/doc/samtools/README.Debian -rw-r--r-- root/root 2479 2024-04-15 14:10 ./usr/share/doc/samtools/README.gz -rw-r--r-- root/root 313 2023-12-15 15:06 ./usr/share/doc/samtools/README.test -rw-r--r-- root/root 2195 2024-05-30 18:52 ./usr/share/doc/samtools/changelog.Debian.gz -rw-r--r-- root/root 36595 2024-04-15 14:10 ./usr/share/doc/samtools/changelog.gz -rw-r--r-- root/root 2250 2024-05-29 13:04 ./usr/share/doc/samtools/copyright drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/doc/samtools/examples/ -rw-r--r-- root/root 1315 2024-04-15 14:10 ./usr/share/doc/samtools/examples/00README.txt -rw-r--r-- root/root 3225 2024-04-15 14:10 ./usr/share/doc/samtools/examples/ex1.fa -rw-r--r-- root/root 114565 2024-05-30 18:52 ./usr/share/doc/samtools/examples/ex1.sam.gz -rw-r--r-- root/root 98 2024-04-15 14:10 ./usr/share/doc/samtools/examples/toy.fa -rw-r--r-- root/root 786 2024-04-15 14:10 ./usr/share/doc/samtools/examples/toy.sam drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 168 2023-12-15 15:06 ./usr/share/lintian/overrides/samtools drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/man/ drwxr-xr-x root/root 0 2024-05-30 18:52 ./usr/share/man/man1/ -rw-r--r-- root/root 462 2024-05-30 18:52 ./usr/share/man/man1/ace2sam.1.gz -rw-r--r-- root/root 1637 2024-05-30 18:52 ./usr/share/man/man1/samtools-addreplacerg.1.gz -rw-r--r-- 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cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 52904 Build-Time: 87 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 7 Job: /srv/debomatic/incoming/samtools_1.20-3.dsc Machine Architecture: amd64 Package: samtools Package-Time: 98 Source-Version: 1.20-3 Space: 52904 Status: successful Version: 1.20-3 -------------------------------------------------------------------------------- Finished at 2024-08-05T01:13:30Z Build needed 00:01:38, 52904k disk space