sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | htslib 1.21+ds-1 (amd64) Mon, 30 Jun 2025 16:31:17 +0000 | +==============================================================================+ Package: htslib Version: 1.21+ds-1 Source Version: 1.21+ds-1 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Mon, 30 Jun 2025 16:31:18 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.21+ds-1 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup htslib_1.21+ds-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 30 Jun 2025 16:31:18 +0000 | +------------------------------------------------------------------------------+ 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 Mon, 30 Jun 2025 16:31:20 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/htslib_1.21+ds-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 30 Jun 2025 16:31:20 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0), build-essential Filtered Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0), build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/htslib-zFYRkP/resolver-0RE7n3/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/htslib-zFYRkP/resolver-0RE7n3/apt_archive ./ InRelease Get:2 copy:/build/htslib-zFYRkP/resolver-0RE7n3/apt_archive ./ Release [609 B] Ign:3 copy:/build/htslib-zFYRkP/resolver-0RE7n3/apt_archive ./ Release.gpg Get:4 copy:/build/htslib-zFYRkP/resolver-0RE7n3/apt_archive ./ Sources [735 B] Get:5 copy:/build/htslib-zFYRkP/resolver-0RE7n3/apt_archive ./ Packages [774 B] Fetched 2118 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 automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhtscodecs-dev libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 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 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user liblzma-doc 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 publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhtscodecs-dev libhtscodecs2 libidn2-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 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 zlib1g-dev 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 28.6 MB/28.9 MB of archives. After this operation, 97.1 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [312 kB] Get:2 copy:/build/htslib-zFYRkP/resolver-0RE7n3/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 B] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:26 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Preconfiguring packages ... Fetched 28.6 MB in 0s (122 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23091 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... 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Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libhtscodecs-dev:amd64 (1.6.1-2) ... Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b1) ... Setting up libssl-dev:amd64 (3.5.0-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up debhelper (13.24.2) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 30 Jun 2025 16:31:27 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 30 Jun 2025 16:31:27 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b1 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.44-3 libblkid1_2.41-5 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcom-err2_1.47.2-3+b1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl3t64-gnutls_8.14.1-2 libcurl4-gnutls-dev_8.14.1-2 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.9-2 libgnutls-openssl27t64_3.8.9-2 libgnutls28-dev_3.8.9-2 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhogweed6t64_3.10.1-1 libhtscodecs-dev_1.6.1-2 libhtscodecs2_1.6.1-2 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libidn2-dev_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma-dev_5.8.1-1 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1 libnghttp2-dev_1.64.0-1.1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsmartcols1_2.41-5 libsqlite3-0_3.46.1-6 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.0-2 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunbound8_1.22.0-1+b1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 nettle-dev_3.10.1-1 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 30 Jun 2025 16:31:27 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: htslib Binary: libhts3t64, libhts-dev, htslib-test, tabix Architecture: any all Version: 1.21+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://github.com/samtools/htslib Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, build-essential Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0) Package-List: htslib-test deb science optional arch=all libhts-dev deb libdevel optional arch=any libhts3t64 deb libs optional arch=any tabix deb science optional arch=any Checksums-Sha1: 40bf7c6cd4fefb1f7b3daef77adfee3f4fcd04e8 1570614 htslib_1.21+ds.orig.tar.bz2 8a2a78fae69e3632b15f3a530d687109d5c2f363 21468 htslib_1.21+ds-1.debian.tar.xz Checksums-Sha256: 679c92270d1538e4a53d31e962017431f5076569729b49a3d0835a6b2228ebd4 1570614 htslib_1.21+ds.orig.tar.bz2 eeb7a20db21dcb35f9aa7ae6a0e9be1f55b1d7da7b5f05e78725031d67cb4899 21468 htslib_1.21+ds-1.debian.tar.xz Files: 386e2801e301f84164b2fb46d30fd049 1570614 htslib_1.21+ds.orig.tar.bz2 c679333c2ac1020b1e4a4ab7be4a28a3 21468 htslib_1.21+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmelJj0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrMexAAkGqhM7giJad5IBKfBYVhpqSXj/VQ hs1q8QfsKEEXg3IWeSTN3mqlAb1RJUkc28Mq79G9rGCArXLfnI7dZpwhaKhD62X7 cy94cfhQSTJdAQ/ByUSy8tQnB4ROYf7SAb6Jy9F/ucT7nhl8x3ixRMbkwIXEUAWc 7DBTOFlDqlkdIQmJWLlpBDKQkWQxjJJAAFfI6PlBz+z4pTUpMGZZH1N+U+NKZK/Q UKlX+2W814vP+8cgeRQukAQXxrpZFQEw+EG5EasM3DiWxug0s/lmm9qef/gliSVj bos2/xe5+HVs6HnJ+bFFy2Qjavs2lMy4F0RtXMjpoJu1yJKYxZD3j+97g86ZIAOu ChFj8xUhwuNuBB1xJISOJnlyJmCCJjCRrF6x/H75rUrBrG5NgEpDMiUkKuVikZCF TNIV7qU5UDYFZHAMAj5vAlUII061MPKI7YClSNreSo3RXRAdWPP7AeWXfMICRH3w qyWbiZ1y9YRMHY5ehKs96RE7xrNo4h0jHjH5LU3aoBsBnRDn0E+YX2jKbvYbLI9W Ut6W6tGKzQuxqb9n41WqiGTMRLkGqmcTLs0c9pGomL3npf+7gMUidOXGfYVlj1Rw 3m3WNCXeREHVMv1h+Sjd+FMpnPrwe+BSZHVw1/VsBOJ+F6SyTyluSM5noFHBKxuW G5NyYnkAUQ3as9k= =ZfTO -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./htslib_1.21+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting htslib in /build/htslib-zFYRkP/htslib-1.21+ds dpkg-source: info: unpacking htslib_1.21+ds.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.21+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 30 Jun 2025 16:31:28 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.21+ds-1 perl-5.40-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network htslib_1.21+ds-1 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=/build/htslib-zFYRkP/htslib-1.21+ds 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-7b5248f1-3432-41a4-bb13-2096acc13d0c SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.21+ds-1 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 htslib-1.21+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_auto_clean make -j2 distclean make[2]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* \ test/longrefs/*.tmp.* test/tabix/*.tmp.* \ test/bgzf_boundaries/*.tmp.* test/*/FAIL* \ header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -rf htscodecs/tests/test.out rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico rm -f hts-object-files rm -f htscodecs/tests/*.o rm -f libhts.a annot-tsv bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/pileup_mod test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_faidx test/test_kfunc test/test_khash test/test_kstring test/test_mod test/test_nibbles test/test_realn test/test-regidx test/test_str2int test/test_time_funcs test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/test-bcf_set_variant_type test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk rm -rf autom4te.cache make[2]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -rf test_backup/ make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3t64/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/ 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 htslib-1.21+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building htslib using existing ./htslib_1.21+ds.orig.tar.bz2 dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building htslib in htslib_1.21+ds-1.debian.tar.xz dpkg-source: info: building htslib in htslib_1.21+ds-1.dsc debian/rules binary dh binary dh_update_autotools_config cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp mv debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3 cp -f /usr/share/misc/config.guess ./config.guess cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp mv debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b cp -f /usr/share/misc/config.sub ./config.sub 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 find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/x86_64-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib' ./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 --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/x86_64-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib 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 ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking whether __get_cpuid_max is declared... yes checking whether __cpuid_count is declared... yes checking C compiler flags needed for sse4.1... -msse4.1 -mssse3 -mpopcnt checking C compiler flags needed for avx2... -mavx2 -mpopcnt checking C compiler flags needed for avx512f... -mavx512f -mpopcnt checking for working __builtin_cpu_supports("ssse3")... yes checking for __attribute__((target))... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for getpagesize... yes checking for working mmap... (cached) yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for __attribute__((constructor))... yes checking for clock_gettime with CLOCK_PROCESS_CPUTIME_ID... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for htscodecs/rANS_static4x16.h... yes checking for rans_compress_bound_4x16 in -lhtscodecs... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_external.mk to htscodecs.mk make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.21" \ libdir=/usr/lib/x86_64-linux-gnu make -j2 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.21 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o header.o header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.21"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2' \ '-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects' \ '-Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ > config_vars.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts_os.o hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multipart.o multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o probaln.o probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o realn.o realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o region.o region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o simd.o simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o textutils.o textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o faidx.pico faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o header.pico header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts.pico hts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o md5.pico md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o realn.pico realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o regidx.pico regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o region.pico region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam.pico sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o simd.pico simd.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o tbx.pico tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/x86_64-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o annot-tsv.o annot-tsv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup.o test/pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_expr.o test/test_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_faidx.o test/test_faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_khash.o test/test_khash.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_mod.o test/test_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_nibbles.o test/test_nibbles.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_index.o test/test_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico simd.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread ln -sf libhts.so libhts.so.3 gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o simd.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_khash test/test_khash.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_nibbles test/test_nibbles.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread make[2]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.21" \ libdir=/usr/lib/x86_64-linux-gnu \ || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j2 test "TESTSUITEFLAGS=-j2 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.21 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' test/hts_endian test/test_expr test/test_kfunc test/test_khash test/test_kstring test/test_nibbles -v test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz -@ 2 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 --threads 2 Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam PASS : $pileup -m mp_overlap1.sam PASS : $pileup -m mp_overlap2.sam Expected passes: 23 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 41 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-MNf1.sam (must exit non-zero) PASS : $test_mod < MM-MNf2.sam (must exit non-zero) PASS : $test_mod < MM-bounds+.sam (must exit non-zero) PASS : $test_mod < MM-bounds-.sam (must exit non-zero) Expected passes: 16 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip --output no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok bgzip --output 4 threads: .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -b -m 14 -x /tmp/8vsFfyjR9F/index.bam.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -b -m 0 -x /tmp/8vsFfyjR9F/index.bam.bai /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -b /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -z -m 14 -x /tmp/8vsFfyjR9F/index.sam.gz.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -z -m 0 -x /tmp/8vsFfyjR9F/index.sam.gz.bai /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -b /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -z -m 14 -x /tmp/8vsFfyjR9F/index.sam.gz.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index_dos.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -z -m 0 -x /tmp/8vsFfyjR9F/index.sam.gz.bai /build/htslib-zFYRkP/htslib-1.21+ds/test/index_dos.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -b /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -C -x /tmp/8vsFfyjR9F/index.cram.crai /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.cram .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index /tmp/8vsFfyjR9F/index.cram .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -b -m 14 -x /tmp/8vsFfyjR9F/index.bcf.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.vcf > /tmp/8vsFfyjR9F/index.bcf .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.bcf .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -z -m 14 -x /tmp/8vsFfyjR9F/index.vcf.gz.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.vcf > /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -l 0 -z -m 0 -x /tmp/8vsFfyjR9F/index.vcf.gz.tbi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.vcf > /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -t /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/tabix /tmp/8vsFfyjR9F/index.vcf.gz##idx##/tmp/8vsFfyjR9F/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 2:2000000-2000000 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/8vsFfyjR9F/index.bam.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -b -m 0 -x /tmp/8vsFfyjR9F/index.bam.bai /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -b /tmp/8vsFfyjR9F/index.bam .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/8vsFfyjR9F/index.sam.gz.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/8vsFfyjR9F/index.sam.gz.bai /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -b /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/8vsFfyjR9F/index.sam.gz.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index_dos.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/8vsFfyjR9F/index.sam.gz.bai /build/htslib-zFYRkP/htslib-1.21+ds/test/index_dos.sam > /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -b /tmp/8vsFfyjR9F/index.sam.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -C -x /tmp/8vsFfyjR9F/index.cram.crai /build/htslib-zFYRkP/htslib-1.21+ds/test/index.sam > /tmp/8vsFfyjR9F/index.cram .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index /tmp/8vsFfyjR9F/index.cram .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -b -m 14 -x /tmp/8vsFfyjR9F/index.bcf.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.vcf > /tmp/8vsFfyjR9F/index.bcf .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.bcf .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 14 -x /tmp/8vsFfyjR9F/index.vcf.gz.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.vcf > /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -@4 -l 0 -z -m 0 -x /tmp/8vsFfyjR9F/index.vcf.gz.tbi /build/htslib-zFYRkP/htslib-1.21+ds/test/index.vcf > /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -t /tmp/8vsFfyjR9F/index.vcf.gz .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/tabix /tmp/8vsFfyjR9F/index.vcf.gz##idx##/tmp/8vsFfyjR9F/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 1:1000000-1000000 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 1:2000000-2000000 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 2:1000000-1000000 .. ok test_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /tmp/8vsFfyjR9F/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing BAM records in multiple BGZF blocks: ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam bgzf_boundaries/bgzf_boundaries1.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries1.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam bgzf_boundaries/bgzf_boundaries2.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries2.bam.tmp.sam ce#1.sam ./test_view -@4 -p bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam bgzf_boundaries/bgzf_boundaries3.bam ./compare_sam.pl bgzf_boundaries/bgzf_boundaries3.bam.tmp.sam ce#1.sam ./test_view -@4 -b -l 0 -p bgzf_boundaries/large_rec.tmp.sam.bam bgzf_boundaries/large_rec.tmp.sam ./test_view -@4 -p bgzf_boundaries/large_rec.tmp.sam.bam.sam bgzf_boundaries/large_rec.tmp.sam.bam ./compare_sam.pl bgzf_boundaries/large_rec.tmp.sam bgzf_boundaries/large_rec.tmp.sam.bam.sam .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 -i reference=ce.fa -M range.cram CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 ./test_view -@4 -M range.bam CHROMOSOME_I:1122-1122 CHROMOSOME_II:1136-1136 CHROMOSOME_II:1241-1241 CHROMOSOME_II:1267-1267 CHROMOSOME_II:1326-1326 CHROMOSOME_II:1345-1345 CHROMOSOME_II:1353-1353 CHROMOSOME_II:1366-1366 CHROMOSOME_II:1416-1416 CHROMOSOME_II:1459-1459 CHROMOSOME_II:1536-1536 > range.tmp ./compare_sam.pl range.tmp range.out2 .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-vcf-api /tmp/8vsFfyjR9F/test-vcf-api.bcf .. ok test_bcf2vcf: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /build/htslib-zFYRkP/htslib-1.21+ds/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-vcf-sweep /tmp/8vsFfyjR9F/test-vcf-api.bcf .. ok test_vcf_various: /build/htslib-zFYRkP/htslib-1.21+ds/htsfile -ch /build/htslib-zFYRkP/htslib-1.21+ds/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /build/htslib-zFYRkP/htslib-1.21+ds/htsfile -c /build/htslib-zFYRkP/htslib-1.21+ds/test/formatcols.vcf .. ok test_vcf_various: /build/htslib-zFYRkP/htslib-1.21+ds/htsfile -c /build/htslib-zFYRkP/htslib-1.21+ds/test/noroundtrip.vcf .. ok test_vcf_various: /build/htslib-zFYRkP/htslib-1.21+ds/htsfile -c /build/htslib-zFYRkP/htslib-1.21+ds/test/formatmissing.vcf .. ok test_vcf_various: /build/htslib-zFYRkP/htslib-1.21+ds/htsfile -c /build/htslib-zFYRkP/htslib-1.21+ds/test/vcf_meta_meta.vcf .. ok test_vcf_various: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view /build/htslib-zFYRkP/htslib-1.21+ds/test/modhdr.vcf.gz chr22:1-2 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 74452500 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 34270147 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 11108528 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 42233895 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 8111117 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 85644070 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 49879942 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 47881429 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 69081244 .. ok test-bcf-sr: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr.pl -t /tmp/8vsFfyjR9F -s 83459376 .. ok test_bcf_sr_no_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.b.vcf /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/8vsFfyjR9F/no_index_1.err .. ok test_bcf_sr_no_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/8vsFfyjR9F/no_index_2.out 2> /tmp/8vsFfyjR9F/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/8vsFfyjR9F/no_index_3.out 2> /tmp/8vsFfyjR9F/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr --no-index -p all --args /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.rec_order.vcf /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/merge.noidx.a.vcf > /tmp/8vsFfyjR9F/no_index_4.out 2> /tmp/8vsFfyjR9F/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -b -p /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf -x /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf.csi /build/htslib-zFYRkP/htslib-1.21+ds/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_1.out.vcf -r '1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_2.out.vcf -r '1:1-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_4.out.vcf -r '1:1-1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_5.out.vcf -r '{1:1}' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_14.out.vcf -t '1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_15.out.vcf -t '1:1-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_17.out.vcf -t '1:1-1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_18.out.vcf -t '{1:1}' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-sr -O vcf -o /tmp/8vsFfyjR9F/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/8vsFfyjR9F/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok test_command: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf-translate - .. ok test_convert_padded_header: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -t ce.fa -C /tmp/8vsFfyjR9F/headernul0.bam .. ok test_convert_padded_header: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -t ce.fa -C /tmp/8vsFfyjR9F/headernul1.bam .. ok test_convert_padded_header: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_view -t ce.fa -C /tmp/8vsFfyjR9F/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /build/htslib-zFYRkP/htslib-1.21+ds/bgzip -I /build/htslib-zFYRkP/htslib-1.21+ds/test/bgziptest.txt.tmp.gz.gzi -c -g /build/htslib-zFYRkP/htslib-1.21+ds/test/bgziptest.txt .. ok test-logging: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/build/htslib-zFYRkP/htslib-1.21+ds /build/htslib-zFYRkP/htslib-1.21+ds/test/with-shlib.sh /build/htslib-zFYRkP/htslib-1.21+ds/htsfile https://localhost:99999/invalid_port .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn01.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -a -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn01.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -a -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -e -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn01.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn01.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -e -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -r -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02-r.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -a -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02_exp.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02.fa -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn02_exp-a.sam -o - .. ok test_realn: /build/htslib-zFYRkP/htslib-1.21+ds/test/test_realn -f /build/htslib-zFYRkP/htslib-1.21+ds/test/realn03.fa -e -i /build/htslib-zFYRkP/htslib-1.21+ds/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /build/htslib-zFYRkP/htslib-1.21+ds/test/test-bcf_set_variant_type .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -c chr,beg,end -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -c chr,beg,end -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl,value:overlap,value -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl,value:overlap,value -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl,value:overlap,value -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -O 0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -O 0.5 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -rO 0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -rO 0.5 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.1.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.2.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.3.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.3.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.3.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl:overlap -a nbp,frac -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.4.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.4.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.4.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.5.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.5.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.5.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.6.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.6.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.6.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.7.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.7.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.7.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.8.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.8.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.8.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.9.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.9.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.9.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -f smpl -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -x -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -x -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -x -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -f smpl -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -f smpl -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -f smpl -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -x -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -x -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.10.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -m smpl -x -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2 -I -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.12.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.12.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.12.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d , -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.12.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.12.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.12.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.12.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -h 0:0 -d $',:\t' -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/dst.11.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5 -r -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0.5,0.5 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 0,1 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -s /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok run_annot_tsv: cat /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt | /build/htslib-zFYRkP/htslib-1.21+ds/annot-tsv -c 1,2,3 -f 4:5 -O 1,0 -t /build/htslib-zFYRkP/htslib-1.21+ds/test/annot-tsv/src.13.txt .. ok Number of tests: total .. 340 passed .. 340 failed .. 0 make[2]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -fr -- /tmp/dh-xdg-rundir-W9Mab_KH make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' echo "Suppress test for Architecture independant builds." Suppress test for Architecture independant builds. make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3t64/ debian/libhts3t64/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/htslib-test/ debian/htslib-test/ debian/.debhelper/generated/tabix/ debian/tabix/ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /build/htslib-zFYRkP/htslib-1.21+ds/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.21" \ libdir=/usr/lib/x86_64-linux-gnu install -m0755 -d /build/htslib-zFYRkP/htslib-1.21\+ds/debian/tmp make -j2 install DESTDIR=/build/htslib-zFYRkP/htslib-1.21\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/htslib-zFYRkP/htslib-1.21+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.21 libdir=/usr/lib/x86_64-linux-gnu make[2]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' mkdir -p -m 755 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/bin /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/include /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/include/htslib /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/share/man/man1 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/share/man/man5 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/share/man/man7 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig if test -n "/usr/lib/x86_64-linux-gnu/htslib"; then mkdir -p -m 755 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 libhts.so /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.21 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/x86_64-linux-gnu#g;s#@-PACKAGE_VERSION@#1.21#g' htslib.pc.tmp > /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc chmod 644 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.21 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so ln -sf libhts.so.1.21 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 install -p annot-tsv bgzip htsfile tabix /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /build/htslib-zFYRkP/htslib-1.21+ds/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals rm -f -r test mv test_backup test make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_install-indep make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_install --indep install -m0755 -d debian/htslib-test/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/tests/run-unit-test debian/htslib-test/usr/share/doc/libhts-dev/ install -m0755 -d debian/htslib-test/usr/share/htslib-test cp --reflink=auto -a ./Makefile ./annot-tsv.c ./bcf_sr_sort.c ./bcf_sr_sort.h ./bgzf.c ./bgzip.c ./config.h ./config.mk ./config_vars.h ./errmod.c ./faidx.c ./fuzz_settings.h ./header.c ./header.h ./hfile.c ./hfile_gcs.c ./hfile_internal.h ./hfile_libcurl.c ./hfile_s3.c ./hfile_s3_write.c ./hts.c ./hts_expr.c ./hts_internal.h ./hts_os.c ./hts_time_funcs.h ./htscodecs.mk ./htscodecs_bundled.mk ./htscodecs_external.mk ./htsfile.c ./htslib.mk ./htslib_static.mk ./htslib_vars.mk ./kfunc.c ./kstring.c ./md5.c ./multipart.c ./os ./plugin.c ./probaln.c ./realn.c ./regidx.c ./region.c ./sam.c ./sam_internal.h ./sam_mods.c ./simd.c ./synced_bcf_reader.c ./tabix.c ./tbx.c ./textutils.c ./textutils_internal.h ./thread_pool.c ./thread_pool_internal.h ./vcf.c ./vcf_sweep.c ./vcfutils.c ./version.h ./version.sh debian/htslib-test/usr/share/htslib-test/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/cram cp --reflink=auto -a ./cram/cram.h ./cram/cram_codecs.c ./cram/cram_codecs.h ./cram/cram_decode.c ./cram/cram_decode.h ./cram/cram_encode.c ./cram/cram_encode.h ./cram/cram_external.c ./cram/cram_index.c ./cram/cram_index.h ./cram/cram_io.c ./cram/cram_io.h ./cram/cram_samtools.h ./cram/cram_stats.c ./cram/cram_stats.h ./cram/cram_structs.h ./cram/mFILE.c ./cram/mFILE.h ./cram/misc.h ./cram/open_trace_file.c ./cram/open_trace_file.h ./cram/os.h ./cram/pooled_alloc.c ./cram/pooled_alloc.h ./cram/string_alloc.c ./cram/string_alloc.h debian/htslib-test/usr/share/htslib-test/cram/ install -m0755 -d debian/htslib-test/usr/share/htslib-test/test cp --reflink=auto -a ./test/annot-tsv ./test/auxf\#values.sam ./test/auxf\#values_java.cram ./test/auxf.fa ./test/auxf.fa.fai ./test/base_mods ./test/bcf-sr ./test/bgzf_boundaries ./test/bgziptest.txt ./test/bgziptest.txt.gz ./test/bgziptest.txt.gz.gzi ./test/c1\#bounds.sam ./test/c1\#clip.sam ./test/c1\#noseq.sam ./test/c1\#pad1.sam ./test/c1\#pad2.sam ./test/c1\#pad3.sam ./test/c1\#unknown.sam ./test/c1.fa ./test/c1.fa.fai ./test/c2\#pad.sam ./test/c2.fa ./test/c2.fa.fai ./test/ce\#1.sam ./test/ce\#1000.sam ./test/ce\#2.sam ./test/ce\#5.sam ./test/ce\#5b.sam ./test/ce\#5b_java.cram ./test/ce\#large_seq.sam ./test/ce\#supp.sam ./test/ce\#tag_depadded.sam ./test/ce\#tag_padded.sam ./test/ce\#unmap.sam ./test/ce\#unmap1.sam ./test/ce\#unmap2.sam ./test/ce.fa ./test/ce.fa.fai ./test/colons.bam ./test/colons.bam.bai ./test/compare_sam.pl ./test/cross_validate.sh ./test/emptyfile ./test/faidx ./test/fastq ./test/fastqs_README.txt ./test/fieldarith.c ./test/fieldarith.sam ./test/formatcols.vcf ./test/formatmissing-out.vcf ./test/formatmissing.vcf ./test/fuzz ./test/header_syms.pl ./test/hfile.c ./test/hts_endian.c ./test/index.bam.bai ./test/index.bam.csi ./test/index.bcf.csi ./test/index.cram.crai ./test/index.sam ./test/index.sam.gz.bai ./test/index.sam.gz.csi ./test/index.vcf ./test/index.vcf.gz.csi ./test/index.vcf.gz.tbi ./test/index2.sam ./test/index_dos.sam ./test/longrefs ./test/maintainer ./test/md\#1.sam ./test/md.fa ./test/md.fa.fai ./test/modhdr.expected.vcf ./test/modhdr.vcf.gz ./test/modhdr.vcf.gz.csi ./test/mpileup ./test/no_hdr_sq_1.bam ./test/no_hdr_sq_1.bam.csi ./test/no_hdr_sq_1.expected.sam ./test/noroundtrip-out.vcf ./test/noroundtrip.vcf ./test/pileup.c ./test/pileup_mod.c ./test/plugins-dlhts.c ./test/range.bam ./test/range.bam.bai ./test/range.cram ./test/range.cram.crai ./test/range.out ./test/range.out2 ./test/realn01.fa ./test/realn01.fa.fai ./test/realn01.sam ./test/realn01_exp-a.sam ./test/realn01_exp-e.sam ./test/realn01_exp.sam ./test/realn02-r.sam ./test/realn02.fa ./test/realn02.fa.fai ./test/realn02.sam ./test/realn02_exp-a.sam ./test/realn02_exp-e.sam ./test/realn02_exp.sam ./test/realn03.fa ./test/realn03.fa.fai ./test/realn03.sam ./test/realn03_exp.sam ./test/sam.c ./test/sam_filter ./test/simple_test_driver.sh ./test/tabix ./test/tabix.out ./test/test-bcf-sr.c ./test/test-bcf-sr.pl ./test/test-bcf-translate.c ./test/test-bcf-translate.out ./test/test-bcf_set_variant_type.c ./test/test-logging.pl ./test/test-parse-reg.c ./test/test-regidx.c ./test/test-vcf-api.c ./test/test-vcf-api.out ./test/test-vcf-hdr-in.vcf ./test/test-vcf-hdr.out ./test/test-vcf-sweep.c ./test/test-vcf-sweep.out ./test/test.pl ./test/test_bgzf.c ./test/test_expr.c ./test/test_faidx.c ./test/test_index.c ./test/test_introspection.c ./test/test_kfunc.c ./test/test_khash.c ./test/test_kstring.c ./test/test_mod.c ./test/test_nibbles.c ./test/test_realn.c ./test/test_str2int.c ./test/test_time_funcs.c ./test/test_view.c ./test/thrash_threads1.c ./test/thrash_threads2.c ./test/thrash_threads3.c ./test/thrash_threads4.c ./test/thrash_threads5.c ./test/thrash_threads6.c ./test/thrash_threads7.c ./test/thread_pool.md ./test/usepublic.cpp ./test/vcf_meta_meta.vcf ./test/with-shlib.sh ./test/xx\#MD.sam ./test/xx\#MD2.sam ./test/xx\#blank.sam ./test/xx\#large_aux.sam ./test/xx\#large_aux2.sam ./test/xx\#large_aux_java.cram ./test/xx\#minimal.sam ./test/xx\#pair.sam ./test/xx\#repeated.sam ./test/xx\#rg.sam ./test/xx\#tlen.sam ./test/xx\#tlen2.sam ./test/xx\#triplet.sam ./test/xx\#unsorted.sam ./test/xx.fa ./test/xx.fa.fai debian/htslib-test/usr/share/htslib-test/test/ sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's#\.\./\.\./htslib/#htslib/#' `grep -Rl '../../htslib/' debian/htslib-test/*` make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_install -Nhtslib-test install -m0755 -d debian/libhts3t64/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/htslib debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.21 debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.3 debian/libhts3t64/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts3t64/usr/share/man/man5 cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man5/ install -m0755 -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -m0755 -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/htslib-test.debhelper.log debian/rules override_dh_installdocs make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_installdocs install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/copyright debian/libhts3t64/usr/share/doc/libhts3t64/copyright install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so: No such file or directory make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_installchangelogs NEWS install -m0755 -d debian/htslib-test/usr/share/doc/htslib-test install -p -m0644 debian/.debhelper/generated/htslib-test/dh_installchangelogs.dch.trimmed debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian install -p -m0644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/.debhelper/generated/libhts3t64/dh_installchangelogs.dch.trimmed debian/libhts3t64/usr/share/doc/libhts3t64/changelog.Debian install -p -m0644 NEWS debian/libhts3t64/usr/share/doc/libhts3t64/changelog install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_installman install -m0755 -d debian/libhts3t64/usr/share/man/man7/ install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 debian/tabix/usr/share/man/man1/tabix.1 mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 debian/tabix/usr/share/man/man1/tabix.1 mv debian/libhts3t64/usr/share/man/man5/faidx.5.dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 mv debian/libhts3t64/usr/share/man/man5/sam.5.dh-new debian/libhts3t64/usr/share/man/man5/sam.5 mv debian/libhts3t64/usr/share/man/man5/vcf.5.dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 mv debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 dh_lintian install -m0755 -d debian/libhts-dev/usr/share/lintian/overrides install -p -m0644 debian/libhts-dev.lintian-overrides debian/libhts-dev/usr/share/lintian/overrides/libhts-dev install -m0755 -d debian/htslib-test/usr/share/lintian/overrides install -p -m0644 debian/htslib-test.lintian-overrides debian/htslib-test/usr/share/lintian/overrides/htslib-test dh_perl mv debian/htslib-test.substvars.new debian/htslib-test.substvars dh_link rm -f debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.3 ln -s libhts.so.1.21 debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so ln -s libhts.so.1.21 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so rm -f debian/htslib-test/usr/share/htslib-test/htscodecs.mk ln -s htscodecs_external.mk debian/htslib-test/usr/share/htslib-test/htscodecs.mk install -m0755 -d debian/tabix/usr/share/man/man1 rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism Using 1738873421 as canonical time Normalizing debian/htslib-test/usr/share/htslib-test/test/modhdr.vcf.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/htslib-test/usr/share/htslib-test/test/bgziptest.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/htslib-test cd debian/libhts3t64 chmod a-x usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian gzip -9nf usr/share/doc/htslib-test/changelog usr/share/doc/htslib-test/changelog.Debian chmod a-x usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 gzip -9nf usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 cd '/build/htslib-zFYRkP/htslib-1.21+ds' cd '/build/htslib-zFYRkP/htslib-1.21+ds' cd debian/tabix cd debian/libhts-dev chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian cd '/build/htslib-zFYRkP/htslib-1.21+ds' cd '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_fixperms find debian/htslib-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/doc -type f -a -true -a ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/htslib-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3t64/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/htslib-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64 -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/libhts3t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix -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/libhts-dev/usr/include debian/libhts-dev/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libhts-dev -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/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_missing make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man dh_missing make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_dwz -a install -m0755 -d debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix install -m0755 -d debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug -- debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.21 dwz: debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.21: DWARF compression not beneficial - old size 970234 new size 992358 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug rm -f debian/htslib-test.debhelper.log debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_strip make[1]: Entering directory '/build/htslib-zFYRkP/htslib-1.21+ds' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e5 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.21 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e5/48c6d048c6575ba61430bb5dc83cd41e4f240b.debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f8 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f8/db85e172ff1759f9f5c85eced76650bda27896.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f8/db85e172ff1759f9f5c85eced76650bda27896.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/f8/db85e172ff1759f9f5c85eced76650bda27896.debug debian/tabix/usr/bin/tabix install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1d objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1d/68e67b2e0a8a091db872c46cb0b19bdb4b7ba7.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e5/48c6d048c6575ba61430bb5dc83cd41e4f240b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.21 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e5/48c6d048c6575ba61430bb5dc83cd41e4f240b.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.21 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/60 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/60/ddf6061823a7febe7ca35d0798ef654cae6682.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/60/ddf6061823a7febe7ca35d0798ef654cae6682.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/60/ddf6061823a7febe7ca35d0798ef654cae6682.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fe/769138fbd50babe0fb56a3f9b1daaaf3d0f378.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fe/769138fbd50babe0fb56a3f9b1daaaf3d0f378.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fe/769138fbd50babe0fb56a3f9b1daaaf3d0f378.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/8c objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/8c/358f054f59cd9e11baa27b333129049b9d97b4.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/8c/358f054f59cd9e11baa27b333129049b9d97b4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/8c/358f054f59cd9e11baa27b333129049b9d97b4.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b/ef4603547390740b11fce9e8af3b4bebaa3574.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b/ef4603547390740b11fce9e8af3b4bebaa3574.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b/ef4603547390740b11fce9e8af3b4bebaa3574.debug debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1d/68e67b2e0a8a091db872c46cb0b19bdb4b7ba7.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip rm -fr debian/libhts3t64/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/libhts3t64/usr/lib/debug objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/1d/68e67b2e0a8a091db872c46cb0b19bdb4b7ba7.debug debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc ln -s libhts3t64 debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc/libhts3t64-dbgsym install -m0755 -d debian/.debhelper/libhts3t64 install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/46 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/46/27b7e081988cfdf8229a78bf4e39ae83607aa3.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/46/27b7e081988cfdf8229a78bf4e39ae83607aa3.debug strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/htsfile objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/46/27b7e081988cfdf8229a78bf4e39ae83607aa3.debug debian/tabix/usr/bin/htsfile install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym install -m0755 -d debian/.debhelper/tabix make[1]: Leaving directory '/build/htslib-zFYRkP/htslib-1.21+ds' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.21+ds)" >> debian/libhts3t64/DEBIAN/shlibs chmod 0644 -- debian/libhts3t64/DEBIAN/shlibs dpkg-gensymbols -plibhts3t64 -Idebian/libhts3t64.symbols -Pdebian/libhts3t64 -edebian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.21 mv debian/.debhelper/generated/libhts3t64/triggers.new debian/.debhelper/generated/libhts3t64/triggers mv debian/libhts3t64.substvars.new debian/libhts3t64.substvars rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars debian/libhts3t64/usr/lib/x86_64-linux-gnu/libhts.so.1.21 debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so dh_installdeb install -m0755 -d debian/libhts3t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3t64/triggers debian/libhts3t64/DEBIAN/triggers install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN install -m0755 -d debian/tabix/DEBIAN dh_gencontrol install -m0755 -d debian/libhts3t64/DEBIAN echo misc:Depends= >> debian/libhts3t64.substvars echo misc:Pre-Depends= >> debian/libhts3t64.substvars install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/.debhelper/libhts3t64/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=libhts3t64-dbgsym "-DDepends=libhts3t64 (= \${binary:Version})" "-DDescription=debug symbols for libhts3t64" "-DBuild-Ids=60ddf6061823a7febe7ca35d0798ef654cae6682 7bef4603547390740b11fce9e8af3b4bebaa3574 8c358f054f59cd9e11baa27b333129049b9d97b4 e548c6d048c6575ba61430bb5dc83cd41e4f240b fe769138fbd50babe0fb56a3f9b1daaaf3d0f378" -DSection=debug -UReplaces -UBreaks install -m0755 -d debian/htslib-test/DEBIAN echo misc:Depends= >> debian/htslib-test.substvars echo misc:Pre-Depends= >> debian/htslib-test.substvars dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -cdebian/control -Pdebian/htslib-test chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -cdebian/control -Pdebian/libhts3t64 chmod 0644 -- debian/htslib-test/DEBIAN/control install -m0755 -d debian/tabix/DEBIAN echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/.debhelper/tabix/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=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=1d68e67b2e0a8a091db872c46cb0b19bdb4b7ba7 4627b7e081988cfdf8229a78bf4e39ae83607aa3 f8db85e172ff1759f9f5c85eced76650bda27896" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -cdebian/control -Pdebian/tabix chmod 0644 -- debian/libhts3t64/DEBIAN/control install -m0755 -d debian/libhts-dev/DEBIAN echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -cdebian/control -Pdebian/libhts-dev chmod 0644 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/libhts-dev/DEBIAN/control dh_md5sums install -m0755 -d debian/libhts3t64/DEBIAN install -m0755 -d debian/htslib-test/DEBIAN cd debian/htslib-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN cd debian/.debhelper/libhts3t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/md5sums install -m0755 -d debian/libhts-dev/DEBIAN cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/htslib-test/DEBIAN/md5sums install -m0755 -d debian/tabix/DEBIAN cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/htslib-test .. dpkg-deb --root-owner-group --build debian/libhts3t64 .. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.21+ds-1_amd64.deb'. dpkg-deb: building package 'htslib-test' in '../htslib-test_1.21+ds-1_all.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root .. dpkg-deb: building package 'libhts3t64-dbgsym' in '../libhts3t64-dbgsym_1.21+ds-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.21+ds-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/tabix .. dpkg-deb: building package 'tabix' in '../tabix_1.21+ds-1_amd64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root .. dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.21+ds-1_amd64.deb'. dpkg-genbuildinfo -O../htslib_1.21+ds-1_amd64.buildinfo dpkg-genchanges -O../htslib_1.21+ds-1_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-source: info: using options from htslib-1.21+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-06-30T16:33:46Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 30 Jun 2025 16:33:47 +0000 | +------------------------------------------------------------------------------+ htslib_1.21+ds-1_amd64.changes: ------------------------------- Format: 1.8 Date: Thu, 06 Feb 2025 21:23:41 +0100 Source: htslib Binary: htslib-test libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: source all amd64 Version: 1.21+ds-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: htslib-test - Test data for HTSlib libhts-dev - development files for the HTSlib libhts3t64 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.21+ds-1) unstable; urgency=medium . * Migrate htslib 1.21 from experimental to unstable. Checksums-Sha1: 69ead2b98c4a942b17504e3aafef45db7371a9f3 1553 htslib_1.21+ds-1.dsc 8a2a78fae69e3632b15f3a530d687109d5c2f363 21468 htslib_1.21+ds-1.debian.tar.xz 4580a76ba1a57e6e0c8d96743b1b6a13703d248f 1163476 htslib-test_1.21+ds-1_all.deb 1208c7e5760a9bc8b5e44a7ffa442d1adf4c201f 8365 htslib_1.21+ds-1_amd64.buildinfo a85f4bed6823bc029cf26ac53787983b2eec3f44 1743284 libhts-dev_1.21+ds-1_amd64.deb 411cf03f30a81887336da74df64171665e5ae491 1313264 libhts3t64-dbgsym_1.21+ds-1_amd64.deb f89b060cc8b28da23deb146a974da263880a6c9b 463412 libhts3t64_1.21+ds-1_amd64.deb 68d65b0cd11b6125d1d6b476dba10c66d0348b5b 3051748 tabix-dbgsym_1.21+ds-1_amd64.deb 1f1c1824e032c8420e6a9c759dd79b23e76fa235 496460 tabix_1.21+ds-1_amd64.deb Checksums-Sha256: c1b2283b181c590b80d232490ef105d93c7efe7bb258a997dcd1101049123c0f 1553 htslib_1.21+ds-1.dsc eeb7a20db21dcb35f9aa7ae6a0e9be1f55b1d7da7b5f05e78725031d67cb4899 21468 htslib_1.21+ds-1.debian.tar.xz 983b8e69614fa28fa2868554a57047fecc4007070a35eb7324a4ce4bf8a2cdf3 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c1b2283b181c590b80d232490ef105d93c7efe7bb258a997dcd1101049123c0f 1553 htslib_1.21+ds-1.dsc 983b8e69614fa28fa2868554a57047fecc4007070a35eb7324a4ce4bf8a2cdf3 1163476 htslib-test_1.21+ds-1_all.deb 7aa4be08bed170af3a63527de0af22e5ba75756c8fbef677dfd356decdcdddf7 1743284 libhts-dev_1.21+ds-1_amd64.deb 5e7e80b4b58829b5db1a40517ff3f5979a0d1a038b34c717723a3100b9bd7887 1313264 libhts3t64-dbgsym_1.21+ds-1_amd64.deb be95c8439b92679763d1a85404a42216f5405c705f648049f1acbbce6bd91fc6 463412 libhts3t64_1.21+ds-1_amd64.deb c2db324d702c0dcb3d8c30303d89e1457b30be6d386bf2614d82f4a49c61785b 3051748 tabix-dbgsym_1.21+ds-1_amd64.deb d7caec6326a5c1b89b21303f33c2314455ce23abb3b381fb1e384f450ede9b11 496460 tabix_1.21+ds-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 30 Jun 2025 16:33:46 +0000 Build-Path: /build/htslib-zFYRkP/htslib-1.21+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), comerr-dev (= 2.1-1.47.2-3+b1), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-5), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.44-3), libblkid1 (= 2.41-5), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcom-err2 (= 1.47.2-3+b1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libcurl3t64-gnutls (= 8.14.1-2), libcurl4-gnutls-dev (= 8.14.1-2), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdeflate-dev (= 1.23-2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.9-2), libgnutls-openssl27t64 (= 3.8.9-2), libgnutls28-dev (= 3.8.9-2), libgnutls30t64 (= 3.8.9-2), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libgssapi-krb5-2 (= 1.21.3-5), libgssrpc4t64 (= 1.21.3-5), libhogweed6t64 (= 3.10.1-1), libhtscodecs-dev (= 1.6.1-2), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 14.2.0-19), libidn2-0 (= 2.3.8-2), libidn2-dev (= 2.3.8-2), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), libk5crypto3 (= 1.21.3-5), libkadm5clnt-mit12 (= 1.21.3-5), libkadm5srv-mit12 (= 1.21.3-5), libkdb5-10t64 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5-dev (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41-5), libldap-dev (= 2.6.10+dfsg-1+b1), libldap2 (= 2.6.10+dfsg-1+b1), liblsan0 (= 14.2.0-19), liblzma-dev (= 5.8.1-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1), libnghttp2-dev (= 1.64.0-1.1), libnghttp3-9 (= 1.8.0-1), libnghttp3-dev (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls-dev (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libngtcp2-dev (= 1.11.0-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libquadmath0 (= 14.2.0-19), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsmartcols1 (= 2.41-5), libsqlite3-0 (= 3.46.1-6), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.0-2), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunbound8 (= 1.22.0-1+b1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libzstd-dev (= 1.5.7+dfsg-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), nettle-dev (= 3.10.1-1), openssl-provider-legacy (= 3.5.0-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) 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="1738873421" +------------------------------------------------------------------------------+ | Package contents Mon, 30 Jun 2025 16:33:47 +0000 | +------------------------------------------------------------------------------+ htslib-test_1.21+ds-1_all.deb ----------------------------- new Debian package, version 2.0. size 1163476 bytes: control archive=11736 bytes. 963 bytes, 23 lines control 36635 bytes, 469 lines md5sums Package: htslib-test Source: htslib Version: 1.21+ds-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 8065 Depends: perl:any Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/samtools/htslib Description: Test data for HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains test files and scripts for the HTSlib. drwxr-xr-x root/root 0 2025-02-06 20:23 ./ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/htslib-test/ -rw-r--r-- root/root 4123 2025-02-06 20:23 ./usr/share/doc/htslib-test/changelog.Debian.gz -rw-r--r-- root/root 38335 2024-09-12 15:06 ./usr/share/doc/htslib-test/changelog.gz -rw-r--r-- root/root 5897 2024-05-29 10:10 ./usr/share/doc/htslib-test/copyright drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 641 2024-02-20 18:45 ./usr/share/doc/libhts-dev/run-unit-test drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/htslib-test/ -rw-r--r-- root/root 48700 2025-02-06 20:23 ./usr/share/htslib-test/Makefile -rw-r--r-- root/root 39269 2024-07-23 13:26 ./usr/share/htslib-test/annot-tsv.c -rw-r--r-- root/root 22986 2021-08-12 11:13 ./usr/share/htslib-test/bcf_sr_sort.c -rw-r--r-- root/root 3869 2019-09-12 21:26 ./usr/share/htslib-test/bcf_sr_sort.h -rw-r--r-- root/root 83159 2024-04-05 09:17 ./usr/share/htslib-test/bgzf.c -rw-r--r-- root/root 29931 2024-08-23 17:26 ./usr/share/htslib-test/bgzip.c -rw-r--r-- root/root 5576 2025-02-06 20:23 ./usr/share/htslib-test/config.h -rw-r--r-- root/root 4249 2025-02-06 20:23 ./usr/share/htslib-test/config.mk -rw-r--r-- root/root 482 2025-02-06 20:23 ./usr/share/htslib-test/config_vars.h drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/htslib-test/cram/ -rw-r--r-- root/root 2420 2020-05-20 23:18 ./usr/share/htslib-test/cram/cram.h -rw-r--r-- root/root 125340 2023-11-16 16:08 ./usr/share/htslib-test/cram/cram_codecs.c -rw-r--r-- root/root 8556 2023-01-20 10:05 ./usr/share/htslib-test/cram/cram_codecs.h -rw-r--r-- root/root 125460 2024-03-07 15:14 ./usr/share/htslib-test/cram/cram_decode.c -rw-r--r-- root/root 4572 2024-03-07 15:14 ./usr/share/htslib-test/cram/cram_decode.h -rw-r--r-- root/root 149456 2024-08-06 13:47 ./usr/share/htslib-test/cram/cram_encode.c -rw-r--r-- root/root 3701 2022-07-19 17:16 ./usr/share/htslib-test/cram/cram_encode.h -rw-r--r-- root/root 33270 2024-09-05 15:21 ./usr/share/htslib-test/cram/cram_external.c -rw-r--r-- root/root 29577 2024-03-07 15:14 ./usr/share/htslib-test/cram/cram_index.c -rw-r--r-- root/root 3866 2020-09-16 09:17 ./usr/share/htslib-test/cram/cram_index.h -rw-r--r-- root/root 176823 2024-04-22 14:44 ./usr/share/htslib-test/cram/cram_io.c -rw-r--r-- root/root 18192 2024-02-06 13:22 ./usr/share/htslib-test/cram/cram_io.h -rw-r--r-- root/root 2911 2021-02-03 10:22 ./usr/share/htslib-test/cram/cram_samtools.h -rw-r--r-- root/root 7055 2023-11-09 17:01 ./usr/share/htslib-test/cram/cram_stats.c -rw-r--r-- root/root 2273 2019-11-19 11:20 ./usr/share/htslib-test/cram/cram_stats.h -rw-r--r-- root/root 29665 2023-11-20 17:23 ./usr/share/htslib-test/cram/cram_structs.h -rw-r--r-- root/root 17233 2020-09-16 09:17 ./usr/share/htslib-test/cram/mFILE.c -rw-r--r-- root/root 3075 2019-11-19 11:20 ./usr/share/htslib-test/cram/mFILE.h -rw-r--r-- root/root 3371 2019-11-19 11:20 ./usr/share/htslib-test/cram/misc.h -rw-r--r-- root/root 13994 2023-03-29 16:35 ./usr/share/htslib-test/cram/open_trace_file.c -rw-r--r-- root/root 5027 2020-01-07 16:06 ./usr/share/htslib-test/cram/open_trace_file.h -rw-r--r-- root/root 6922 2025-02-06 20:23 ./usr/share/htslib-test/cram/os.h -rw-r--r-- root/root 5049 2020-01-07 16:06 ./usr/share/htslib-test/cram/pooled_alloc.c -rw-r--r-- root/root 2185 2019-11-19 11:20 ./usr/share/htslib-test/cram/pooled_alloc.h -rw-r--r-- root/root 4422 2020-09-16 09:17 ./usr/share/htslib-test/cram/string_alloc.c -rw-r--r-- root/root 2356 2019-11-19 11:20 ./usr/share/htslib-test/cram/string_alloc.h -rw-r--r-- root/root 6757 2019-11-19 11:20 ./usr/share/htslib-test/errmod.c -rw-r--r-- root/root 30982 2024-08-15 14:18 ./usr/share/htslib-test/faidx.c -rw-r--r-- root/root 1442 2023-08-07 08:39 ./usr/share/htslib-test/fuzz_settings.h -rw-r--r-- root/root 81905 2024-04-29 14:17 ./usr/share/htslib-test/header.c -rw-r--r-- root/root 10466 2020-01-08 16:24 ./usr/share/htslib-test/header.h -rw-r--r-- root/root 40918 2024-08-12 08:38 ./usr/share/htslib-test/hfile.c -rw-r--r-- root/root 5139 2021-06-22 10:24 ./usr/share/htslib-test/hfile_gcs.c -rw-r--r-- root/root 8112 2022-05-13 15:25 ./usr/share/htslib-test/hfile_internal.h -rw-r--r-- root/root 49210 2024-04-29 14:17 ./usr/share/htslib-test/hfile_libcurl.c -rw-r--r-- root/root 41232 2024-04-05 09:17 ./usr/share/htslib-test/hfile_s3.c -rw-r--r-- root/root 24158 2024-04-29 14:17 ./usr/share/htslib-test/hfile_s3_write.c -rw-r--r-- root/root 169061 2024-08-22 13:16 ./usr/share/htslib-test/hts.c -rw-r--r-- root/root 28501 2024-08-15 14:18 ./usr/share/htslib-test/hts_expr.c -rw-r--r-- root/root 5677 2024-07-18 01:25 ./usr/share/htslib-test/hts_internal.h -rw-r--r-- root/root 1981 2021-02-03 10:22 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control 2420 bytes, 37 lines md5sums Package: libhts-dev Source: htslib Version: 1.21+ds-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 7443 Depends: libbz2-dev, libhts3t64 (= 1.21+ds-1), libcurl4-gnutls-dev, libdeflate-dev, liblzma-dev, zlib1g-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: development files for the HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains development files for the HTSlib: headers, static library, manual pages, etc. . 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Package: libhts3t64-dbgsym Source: htslib Version: 1.21+ds-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1382 Depends: libhts3t64 (= 1.21+ds-1) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libhts3t64 Build-Ids: 60ddf6061823a7febe7ca35d0798ef654cae6682 7bef4603547390740b11fce9e8af3b4bebaa3574 8c358f054f59cd9e11baa27b333129049b9d97b4 e548c6d048c6575ba61430bb5dc83cd41e4f240b fe769138fbd50babe0fb56a3f9b1daaaf3d0f378 drwxr-xr-x root/root 0 2025-02-06 20:23 ./ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.build-id/60/ -rw-r--r-- root/root 38664 2025-02-06 20:23 ./usr/lib/debug/.build-id/60/ddf6061823a7febe7ca35d0798ef654cae6682.debug drwxr-xr-x root/root 0 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2025-02-06 20:23 ./usr/share/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-02-06 20:23 ./usr/share/doc/libhts3t64-dbgsym -> libhts3t64 libhts3t64_1.21+ds-1_amd64.deb ------------------------------ new Debian package, version 2.0. size 463412 bytes: control archive=6160 bytes. 1296 bytes, 24 lines control 881 bytes, 12 lines md5sums 33 bytes, 1 lines shlibs 30649 bytes, 945 lines symbols 68 bytes, 2 lines triggers Package: libhts3t64 Source: htslib Version: 1.21+ds-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1120 Depends: libbz2-1.0, libc6 (>= 2.34), libcurl3t64-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), libssl3t64 (>= 3.0.0), zlib1g (>= 1:1.1.4) Breaks: ivar (<< 1.3.1~), libhts-dev (<< 1.13~), libhts3 (<< 1.21+ds-1), libtabixpp (<< 1.0.0-5~), samtools (<< 1.17~) Replaces: libhts-dev (<< 1.13~), libhts3 Provides: libhts3 (= 1.21+ds-1) Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. drwxr-xr-x root/root 0 2025-02-06 20:23 ./ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/htslib/ -rw-r--r-- root/root 14408 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/htslib/hfile_gcs.so -rw-r--r-- root/root 38984 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/htslib/hfile_libcurl.so -rw-r--r-- root/root 38984 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3.so -rw-r--r-- root/root 22600 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/htslib/hfile_s3_write.so -rw-r--r-- root/root 919664 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/libhts.so.1.21 lrwxrwxrwx root/root 0 2025-02-06 20:23 ./usr/lib/x86_64-linux-gnu/libhts.so.3 -> libhts.so.1.21 drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/libhts3t64/ -rw-r--r-- root/root 4123 2025-02-06 20:23 ./usr/share/doc/libhts3t64/changelog.Debian.gz -rw-r--r-- root/root 38335 2024-09-12 15:06 ./usr/share/doc/libhts3t64/changelog.gz -rw-r--r-- root/root 5897 2024-05-29 10:10 ./usr/share/doc/libhts3t64/copyright drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/man/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2025-02-06 20:23 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1537 2025-02-06 20:23 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1857 2025-02-06 20:23 ./usr/share/man/man5/vcf.5.gz drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/man/man7/ -rw-r--r-- root/root 3419 2025-02-06 20:23 ./usr/share/man/man7/htslib-s3-plugin.7.gz tabix-dbgsym_1.21+ds-1_amd64.deb -------------------------------- new Debian package, version 2.0. size 3051748 bytes: control archive=704 bytes. 450 bytes, 12 lines control 400 bytes, 4 lines md5sums Package: tabix-dbgsym Source: htslib Version: 1.21+ds-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3537 Depends: tabix (= 1.21+ds-1) Section: debug Priority: optional Description: debug symbols for tabix Build-Ids: 1d68e67b2e0a8a091db872c46cb0b19bdb4b7ba7 4627b7e081988cfdf8229a78bf4e39ae83607aa3 f8db85e172ff1759f9f5c85eced76650bda27896 drwxr-xr-x root/root 0 2025-02-06 20:23 ./ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.build-id/1d/ -rw-r--r-- root/root 1005584 2025-02-06 20:23 ./usr/lib/debug/.build-id/1d/68e67b2e0a8a091db872c46cb0b19bdb4b7ba7.debug drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.build-id/46/ -rw-r--r-- root/root 1242432 2025-02-06 20:23 ./usr/lib/debug/.build-id/46/27b7e081988cfdf8229a78bf4e39ae83607aa3.debug drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.build-id/f8/ -rw-r--r-- root/root 1277248 2025-02-06 20:23 ./usr/lib/debug/.build-id/f8/db85e172ff1759f9f5c85eced76650bda27896.debug drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 78936 2025-02-06 20:23 ./usr/lib/debug/.dwz/x86_64-linux-gnu/tabix.debug drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-02-06 20:23 ./usr/share/doc/tabix-dbgsym -> tabix tabix_1.21+ds-1_amd64.deb ------------------------- new Debian package, version 2.0. size 496460 bytes: control archive=1128 bytes. 985 bytes, 20 lines control 545 bytes, 9 lines md5sums Package: tabix Source: htslib Version: 1.21+ds-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2336 Depends: libbz2-1.0, libc6 (>= 2.34), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: generic indexer for TAB-delimited genome position files Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosome), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name. . This package is built from the HTSlib source, and provides the bgzip, htsfile, and tabix tools. drwxr-xr-x root/root 0 2025-02-06 20:23 ./ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/bin/ -rwxr-xr-x root/root 678344 2025-02-06 20:23 ./usr/bin/bgzip -rwxr-xr-x root/root 809384 2025-02-06 20:23 ./usr/bin/htsfile -rwxr-xr-x root/root 833960 2025-02-06 20:23 ./usr/bin/tabix drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/doc/tabix/ -rw-r--r-- root/root 4123 2025-02-06 20:23 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 38335 2024-09-12 15:06 ./usr/share/doc/tabix/changelog.gz -rw-r--r-- root/root 5897 2024-05-29 10:10 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/man/ drwxr-xr-x root/root 0 2025-02-06 20:23 ./usr/share/man/man1/ -rw-r--r-- root/root 3063 2025-02-06 20:23 ./usr/share/man/man1/bgzip.1.gz -rw-r--r-- root/root 1918 2025-02-06 20:23 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 3421 2025-02-06 20:23 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 30 Jun 2025 16:33:49 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 30 Jun 2025 16:33:49 +0000 | +------------------------------------------------------------------------------+ Purging /build/htslib-zFYRkP Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 30 Jun 2025 16:33:50 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 95364 Build-Time: 138 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 7 Job: /srv/debomatic/incoming/htslib_1.21+ds-1.dsc Machine Architecture: amd64 Package: htslib Package-Time: 149 Source-Version: 1.21+ds-1 Space: 95364 Status: successful Version: 1.21+ds-1 -------------------------------------------------------------------------------- Finished at 2025-06-30T16:33:46Z Build needed 00:02:29, 95364k disk space