htslib →
1.18+ds-1 →
armhf → 2023-11-10 05:27:22
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| htslib 1.18+ds-1 (armhf) Fri, 10 Nov 2023 05:25:02 +0000 |
+==============================================================================+
Package: htslib
Version: 1.18+ds-1
Source Version: 1.18+ds-1
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-e8ae3587-0258-4ed4-aadf-99ffe73ebc2c' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/htslib-qlU46J/resolver-Po6clj' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.2 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.9 MB]
Fetched 29.1 MB in 5s (5646 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'htslib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/htslib.git
Please use:
git clone https://salsa.debian.org/med-team/htslib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1492 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main htslib 1.18+ds-1 (dsc) [2437 B]
Get:2 http://172.17.4.1/private trixie-staging/main htslib 1.18+ds-1 (tar) [1469 kB]
Get:3 http://172.17.4.1/private trixie-staging/main htslib 1.18+ds-1 (diff) [20.1 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/htslib-qlU46J/htslib-1.18+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-qlU46J' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0), build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0), build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [730 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [762 B]
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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 debhelper
dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libdpkg-perl libelf1 libfile-stripnondeterminism-perl
libhtscodecs-dev libhtscodecs2 libicu72 liblzma-dev libmagic-mgc libmagic1
libnghttp2-14 libpipeline1 libpsl5 librtmp1 libssh2-1 libssl-dev
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make debian-keyring
gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc
libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev pkg-config git bzr liblzma-doc libssl-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
libalgorithm-merge-perl curl | wget | lynx bzip2-doc ca-certificates
libfile-fcntllock-perl libarchive-cpio-perl publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libfile-stripnondeterminism-perl libhtscodecs-dev
libhtscodecs2 libicu72 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libssh2-1 libssl-dev libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
dpkg-dev libdpkg-perl
2 upgraded, 46 newly installed, 0 to remove and 11 not upgraded.
1 not fully installed or removed.
Need to get 26.0 MB/28.0 MB of archives.
After this operation, 90.0 MB of additional disk space will be used.
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Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
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Get:16 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.7 [82.1 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.7 [956 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.4.0-2+rpi1 [358 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.4.0-2+rpi1 [441 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.2-1 [60.0 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs-dev armhf 1.5.2-1 [2958 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.4-0.1 [269 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libssl-dev armhf 3.0.11-1 [2105 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
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Setting up libtool (2.4.7-7) ...
Setting up libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Setting up libcurl4-gnutls-dev:armhf (8.4.0-2+rpi1) ...
Setting up dpkg-dev (1.22.1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.7) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.2-5 bsdutils_1:2.39.2-5 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.7 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-13 gettext-base_0.21-13 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.2-5 libbrotli1_1.0.9-2+b3 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.4.0-2+rpi1 libcurl4-gnutls-dev_8.4.0-2+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.271 libdebhelper-perl_13.11.7 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-4 libhogweed6_3.9.1-2 libhtscodecs-dev_1.5.2-1 libhtscodecs2_1.5.2-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-4 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-4 libkrb5support0_1.20.1-4 libksba8_1.6.4-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblocale-gettext-perl_1.07-6 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.4-0.1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-5 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.25.0-5 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.2-5 libsqlite3-0_3.43.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl-dev_3.0.11-1 libssl3_3.0.11-1 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.09-4 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.2-5 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.11.2-3 mawk_1.3.4.20230808-1 mount_2.39.2-5 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-3 tar_1.34+dfsg-1.2 tzdata_2023c-10 usr-is-merged_37 util-linux_2.39.2-5 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: htslib
Binary: libhts3, libhts-dev, htslib-test, tabix
Architecture: any all
Version: 1.18+ds-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Michael R. Crusoe <crusoe@debian.org>, Steffen Moeller <moeller@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/samtools/htslib
Standards-Version: 4.6.2
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: 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
libhts3 deb libs optional arch=any
tabix deb science optional arch=any
Checksums-Sha1:
48c071f82871471b8b206a1d2879a7732832c0e0 1469485 htslib_1.18+ds.orig.tar.bz2
06ef58c96bffd288e743c7a84ef61d2db3540c66 20136 htslib_1.18+ds-1.debian.tar.xz
Checksums-Sha256:
3d2536366b273a7add9cd98041e26b32a58466613a7017c0e2ee95e871dd7ee3 1469485 htslib_1.18+ds.orig.tar.bz2
a00dc3fe4177b10919835976c3635ee42b02c89382b28503fda77fb1978f4043 20136 htslib_1.18+ds-1.debian.tar.xz
Files:
177115da7d2acc4cc41a4e7abd0a3da0 1469485 htslib_1.18+ds.orig.tar.bz2
568c9ee6a51e718899ffde8b57cd56e6 20136 htslib_1.18+ds-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
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-----END PGP SIGNATURE-----
gpgv: Signature made Tue Nov 7 20:35:25 2023 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./htslib_1.18+ds-1.dsc: no acceptable signature found
dpkg-source: info: extracting htslib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking htslib_1.18+ds.orig.tar.bz2
dpkg-source: info: unpacking htslib_1.18+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 cram_to_bam_export.patch
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
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-e8ae3587-0258-4ed4-aadf-99ffe73ebc2c
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package htslib
dpkg-buildpackage: info: source version 1.18+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from htslib-1.18+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 '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* test/faidx/FAIL* \
test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/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 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_kstring test/test_mod 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 '/<<PKGBUILDDIR>>'
rm -rf test_backup/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files
rm -fr -- debian/libhts3/ 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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
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 '/<<PKGBUILDDIR>>'
# 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/arm-linux-gnueabihf/htslib' \
--with-external-htscodecs \
--with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib'
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/arm-linux-gnueabihf/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/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... /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 C compiler flags needed for ssse3... none
checking C compiler flags needed for popcnt... none
checking C compiler flags needed for sse4.1... none
checking C compiler flags needed for avx2... none
checking C compiler flags needed for avx512f... none
checking for pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
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... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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 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 '/<<PKGBUILDDIR>>'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
PACKAGE_VERSION="1.18" \
libdir=/usr/lib/arm-linux-gnueabihf
make -j4 "CFLAGS=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.18 libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 "1.18"' > 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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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/arm-linux-gnueabihf/htslib\" -c -o plugin.o plugin.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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/arm-linux-gnueabihf/htslib\" -fPIC -c -o plugin.pico plugin.c
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 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
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
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/test_time_funcs test/test_time_funcs.o
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
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 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 -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/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 -lz -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 -lz -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 -lz -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 -lz -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 -lz -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_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 -lz -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 -lz -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 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 '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
PACKAGE_VERSION="1.18" \
libdir=/usr/lib/arm-linux-gnueabihf \
|| \
if find . -name "FAIL*" > /dev/null ; then \
for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \
fi
make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.18 libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
test/hts_endian
test/test_expr
test/test_kfunc
test/test_kstring
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 '^@'
Expected passes: 17
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
Expected passes: 14
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
Expected passes: 21
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)
Expected passes: 12
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 round-trip 4 threads: .. ok
bgzip text mode round-trip 4 threads: .. ok
bgzip -b 4 threads: .. ok
bgzip -b -I 4 threads: .. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -b -m 14 -x /tmp/pOWqcwdVze/index.bam.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -b -m 0 -x /tmp/pOWqcwdVze/index.bam.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -b /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -z -m 14 -x /tmp/pOWqcwdVze/index.sam.gz.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -z -m 0 -x /tmp/pOWqcwdVze/index.sam.gz.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -b /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -z -m 14 -x /tmp/pOWqcwdVze/index.sam.gz.csi /<<PKGBUILDDIR>>/test/index_dos.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -z -m 0 -x /tmp/pOWqcwdVze/index.sam.gz.bai /<<PKGBUILDDIR>>/test/index_dos.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -b /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -C -x /tmp/pOWqcwdVze/index.cram.crai /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.cram
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index /tmp/pOWqcwdVze/index.cram
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -b -m 14 -x /tmp/pOWqcwdVze/index.bcf.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/pOWqcwdVze/index.bcf
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.bcf
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -z -m 14 -x /tmp/pOWqcwdVze/index.vcf.gz.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -l 0 -z -m 0 -x /tmp/pOWqcwdVze/index.vcf.gz.tbi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -t /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/tabix /tmp/pOWqcwdVze/index.vcf.gz##idx##/tmp/pOWqcwdVze/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/index2.bam 1:1000000-1000000
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/index2.bam 1:2000000-2000000
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/index2.bam 2:1000000-1000000
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/index2.bam 2:2000000-2000000
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/pOWqcwdVze/index.bam.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -b -m 0 -x /tmp/pOWqcwdVze/index.bam.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -b /tmp/pOWqcwdVze/index.bam
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/pOWqcwdVze/index.sam.gz.csi /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/pOWqcwdVze/index.sam.gz.bai /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -b /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/pOWqcwdVze/index.sam.gz.csi /<<PKGBUILDDIR>>/test/index_dos.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/pOWqcwdVze/index.sam.gz.bai /<<PKGBUILDDIR>>/test/index_dos.sam > /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -b /tmp/pOWqcwdVze/index.sam.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -C -x /tmp/pOWqcwdVze/index.cram.crai /<<PKGBUILDDIR>>/test/index.sam > /tmp/pOWqcwdVze/index.cram
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index /tmp/pOWqcwdVze/index.cram
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/pOWqcwdVze/index.bcf.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/pOWqcwdVze/index.bcf
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.bcf
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/pOWqcwdVze/index.vcf.gz.csi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -c /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/pOWqcwdVze/index.vcf.gz.tbi /<<PKGBUILDDIR>>/test/index.vcf > /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_index -t /tmp/pOWqcwdVze/index.vcf.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/tabix /tmp/pOWqcwdVze/index.vcf.gz##idx##/tmp/pOWqcwdVze/index.vcf.gz.tbi 1:10000060-10000060
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/index2.bam 1:1000000-1000000
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/index2.bam 1:2000000-2000000
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/index2.bam 2:1000000-1000000
.. ok
test_index:
/<<PKGBUILDDIR>>/test/test_view /tmp/pOWqcwdVze/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 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
.. 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:
/<<PKGBUILDDIR>>/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 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
.. 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:
/<<PKGBUILDDIR>>/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:
/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/pOWqcwdVze/test-vcf-api.bcf
[W::bcf_record_check] Bad BCF record at 1:1: No REF allele
[E::bcf_index_build3] TBI indices for BCF files are not supported
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pOWqcwdVze/test-vcf-api.bcf'
.. ok
test_bcf2vcf:
/<<PKGBUILDDIR>>/test/test_view /<<PKGBUILDDIR>>/test/tabix/vcf_file.bcf
.. ok
test_vcf_sweep:
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/pOWqcwdVze/test-vcf-api.bcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -ch /<<PKGBUILDDIR>>/test/test-vcf-hdr-in.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatcols.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/noroundtrip.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/formatmissing.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/htsfile -c /<<PKGBUILDDIR>>/test/vcf_meta_meta.vcf
.. ok
test_vcf_various:
/<<PKGBUILDDIR>>/test/test_view /<<PKGBUILDDIR>>/test/modhdr.vcf.gz chr22:1-2
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 74452500
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 34270147
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 11108528
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 42233895
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 8111117
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 85644070
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 49879942
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 47881429
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 69081244
.. ok
test-bcf-sr:
/<<PKGBUILDDIR>>/test/test-bcf-sr.pl -t /tmp/pOWqcwdVze -s 83459376
.. ok
test_bcf_sr_no_index:
/<<PKGBUILDDIR>>/test/test-bcf-sr --no-index -p all --args /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.a.vcf /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.b.vcf /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/pOWqcwdVze/no_index_1.err
.. ok
test_bcf_sr_no_index:
/<<PKGBUILDDIR>>/test/test-bcf-sr --no-index -p all --args /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.a.vcf /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/pOWqcwdVze/no_index_2.out 2> /tmp/pOWqcwdVze/no_index_2.err (expected fail)
.. ok
test_bcf_sr_no_index:
/<<PKGBUILDDIR>>/test/test-bcf-sr --no-index -p all --args /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.a.vcf /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/pOWqcwdVze/no_index_3.out 2> /tmp/pOWqcwdVze/no_index_3.err (expected fail)
.. ok
test_bcf_sr_no_index:
/<<PKGBUILDDIR>>/test/test-bcf-sr --no-index -p all --args /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.rec_order.vcf /<<PKGBUILDDIR>>/test/bcf-sr/merge.noidx.a.vcf > /tmp/pOWqcwdVze/no_index_4.out 2> /tmp/pOWqcwdVze/no_index_4.err (expected fail)
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test_view -b -p /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf -x /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf.csi /<<PKGBUILDDIR>>/test/bcf-sr/weird-chr-names.vcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_1.out.vcf -r '1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_2.out.vcf -r '1:1-2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_4.out.vcf -r '1:1-1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_5.out.vcf -r '{1:1}' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/pOWqcwdVze/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:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_14.out.vcf -t '1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_15.out.vcf -t '1:1-2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_17.out.vcf -t '1:1-1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_18.out.vcf -t '{1:1}' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/pOWqcwdVze/weird-chr-names.vcf.bcf
.. ok
test_bcf_sr_range:
/<<PKGBUILDDIR>>/test/test-bcf-sr -O vcf -o /tmp/pOWqcwdVze/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/pOWqcwdVze/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:
/<<PKGBUILDDIR>>/test/test-bcf-translate -
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/pOWqcwdVze/headernul0.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/pOWqcwdVze/headernul1.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/pOWqcwdVze/headernul678.bam
.. ok
test_rebgzip: Alternate zlib/deflate library detected
test_rebgzip:
/<<PKGBUILDDIR>>/bgzip -I /<<PKGBUILDDIR>>/test/bgziptest.txt.tmp.gz.gzi -c -g /<<PKGBUILDDIR>>/test/bgziptest.txt
.. ok
test-logging:
/<<PKGBUILDDIR>>/test/test-logging.pl
.. ok
test_plugin_loading:
HTS_PATH=/<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test/with-shlib.sh /<<PKGBUILDDIR>>/htsfile https://localhost:99999/invalid_port
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn01.fa -i /<<PKGBUILDDIR>>/test/realn01.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -e -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -r -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02-r.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -a -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn02.fa -i /<<PKGBUILDDIR>>/test/realn02_exp-a.sam -o -
.. ok
test_realn:
/<<PKGBUILDDIR>>/test/test_realn -f /<<PKGBUILDDIR>>/test/realn03.fa -e -i /<<PKGBUILDDIR>>/test/realn03.sam -o -
.. ok
test-bcf_set_variant_type:
/<<PKGBUILDDIR>>/test/test-bcf_set_variant_type
.. ok
Number of tests:
total .. 211
passed .. 211
failed .. 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -fr -- /tmp/dh-xdg-rundir-zvtrxjfZ
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
rm -f -- debian/libhts3.substvars debian/libhts-dev.substvars debian/tabix.substvars
rm -fr -- debian/.debhelper/generated/libhts3/ debian/libhts3/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
rm /<<PKGBUILDDIR>>/test/${binary} ; \
done
dh_auto_install -- prefix=/usr \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
PACKAGE_VERSION="1.18" \
libdir=/usr/lib/arm-linux-gnueabihf
install -m0755 -d /<<BUILDDIR>>/htslib-1.18\+ds/debian/tmp
make -j4 install DESTDIR=/<<BUILDDIR>>/htslib-1.18\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -Wdate-time -D_FORTIFY_SOURCE=2" PACKAGE_VERSION=1.18 libdir=/usr/lib/arm-linux-gnueabihf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/include /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man7 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig
if test -n "/usr/lib/arm-linux-gnueabihf/htslib"; then mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/htslib; fi
install -p -m 644 libhts.so /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.18
sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.18#g' htslib.pc.tmp > /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
ln -sf libhts.so.1.18 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so
ln -sf libhts.so.1.18 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3
chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
install -p bgzip htsfile tabix /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/htslib; fi
install -p -m 644 htslib/*.h /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a
install -p -m 644 bgzip.1 htsfile.1 tabix.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p -m 644 faidx.5 sam.5 vcf.5 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5
install -p -m 644 htslib-s3-plugin.7 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man7
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# 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 '/<<PKGBUILDDIR>>'
dh_install -a
install -m0755 -d debian/libhts3/usr/lib/arm-linux-gnueabihf
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/htslib debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.18 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 debian/libhts3/usr/lib/arm-linux-gnueabihf/
install -m0755 -d debian/libhts3/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/libhts3/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/arm-linux-gnueabihf
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so debian/libhts-dev/usr/lib/arm-linux-gnueabihf/
install -m0755 -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig/
install -m0755 -d debian/tabix/usr/bin
cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installdocs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installdocs
install -m0755 -d debian/libhts3/usr/share/doc/libhts3
install -p -m0644 debian/copyright debian/libhts3/usr/share/doc/libhts3/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/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/arm-linux-gnueabihf/libhts.so: No such file or directory
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS
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/libhts3/usr/share/doc/libhts3
install -p -m0644 debian/.debhelper/generated/libhts3/dh_installchangelogs.dch.trimmed debian/libhts3/usr/share/doc/libhts3/changelog.Debian
install -p -m0644 NEWS debian/libhts3/usr/share/doc/libhts3/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 '/<<PKGBUILDDIR>>'
dh_installman -a
install -m0755 -d debian/libhts3/usr/share/man/man7/
install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3/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/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5
man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3/usr/share/man/man5/vcf.5 debian/libhts3/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
man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.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/tabix.1
mv debian/libhts3/usr/share/man/man5/vcf.5.dh-new debian/libhts3/usr/share/man/man5/vcf.5
mv debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
chmod 0644 -- debian/libhts3/usr/share/man/man5/vcf.5 debian/libhts3/usr/share/man/man7/htslib-s3-plugin.7
mv debian/libhts3/usr/share/man/man5/faidx.5.dh-new debian/libhts3/usr/share/man/man5/faidx.5
mv debian/libhts3/usr/share/man/man5/sam.5.dh-new debian/libhts3/usr/share/man/man5/sam.5
chmod 0644 -- debian/libhts3/usr/share/man/man5/faidx.5 debian/libhts3/usr/share/man/man5/sam.5
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
chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1
dh_perl -a
dh_link -a
rm -f debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
ln -s libhts.so.1.18 debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.3
rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
ln -s libhts.so.1.18 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so
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 -a
dh_compress -a
cd debian/libhts3
cd debian/libhts-dev
cd debian/tabix
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
chmod a-x usr/share/doc/libhts3/changelog usr/share/doc/libhts3/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/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/libhts3/changelog usr/share/doc/libhts3/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/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
cd '/<<PKGBUILDDIR>>'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian/libhts3 ! -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 ! -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/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/libhts3/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts3/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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
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/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/libhts3/usr/share/man -type f -a -true -a -true -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/libhts3 -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 -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/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/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/libhts3/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
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 '/<<PKGBUILDDIR>>'
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_missing
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# 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 '/<<PKGBUILDDIR>>'
dh_dwz -a
install -m0755 -d debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug -- debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.18
install -m0755 -d debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf
dwz -mdebian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
dwz: debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.18: DWARF compression not beneficial - old size 832220 new size 852135
objcopy --compress-debug-sections debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug
chmod 0644 -- debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug
objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
rm -f debian/libhts-dev.debhelper.log debian/libhts3.debhelper.log debian/tabix.debhelper.log
debian/rules override_dh_strip
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# This is apparently important for the interpretation by ldc2 in sambamba
dh_strip -Xlibhts.a
install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0f
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0f/07c02d75ea01e2dc6da27f18ffaf0dbc7f5047.debug
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/ec
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.18 debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/ec/6ba8bcdf4a95d6908fb26f1c04bb659cb4225f.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0f/07c02d75ea01e2dc6da27f18ffaf0dbc7f5047.debug
strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip
objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/0f/07c02d75ea01e2dc6da27f18ffaf0dbc7f5047.debug debian/tabix/usr/bin/bgzip
install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/33
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/33/216e1cfffb3239b20682337e4852751b240a02.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/ec/6ba8bcdf4a95d6908fb26f1c04bb659cb4225f.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.18
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/ec/6ba8bcdf4a95d6908fb26f1c04bb659cb4225f.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.18
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/f2
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/f2/09f78e63f8581c3c029aec9a5737caa92c5dfb.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/f2/09f78e63f8581c3c029aec9a5737caa92c5dfb.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/f2/09f78e63f8581c3c029aec9a5737caa92c5dfb.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bf
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bf/4c199c52d746c4d0972628111833e07797e181.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bf/4c199c52d746c4d0972628111833e07797e181.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/bf/4c199c52d746c4d0972628111833e07797e181.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5f
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5f/0254dd32344e320e1295109d40ca7d31294722.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5f/0254dd32344e320e1295109d40ca7d31294722.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/5f/0254dd32344e320e1295109d40ca7d31294722.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/96
objcopy --only-keep-debug --compress-debug-sections debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/96/aa74da074b850c7fdd2a3d2fcf73fe4d7a6e3e.debug
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/96/aa74da074b850c7fdd2a3d2fcf73fe4d7a6e3e.debug
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
objcopy --add-gnu-debuglink debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.build-id/96/aa74da074b850c7fdd2a3d2fcf73fe4d7a6e3e.debug debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/libhts3/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/libhts3/dbgsym-root/usr/lib/debug/.dwz
rm -fr debian/libhts3/usr/lib/debug/.dwz
rmdir -p --ignore-fail-on-non-empty debian/libhts3/usr/lib/debug
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/usr/share/doc
ln -s libhts3 debian/.debhelper/libhts3/dbgsym-root/usr/share/doc/libhts3-dbgsym
install -m0755 -d debian/.debhelper/libhts3
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/33/216e1cfffb3239b20682337e4852751b240a02.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/33/216e1cfffb3239b20682337e4852751b240a02.debug debian/tabix/usr/bin/htsfile
install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/ca
objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/ca/8fa30bd452c7260014025acb52bf08ca3458ac.debug
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/ca/8fa30bd452c7260014025acb52bf08ca3458ac.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/ca/8fa30bd452c7260014025acb52bf08ca3458ac.debug debian/tabix/usr/bin/tabix
install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz
cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf 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 '/<<PKGBUILDDIR>>'
dh_makeshlibs -a
rm -f debian/libhts3/DEBIAN/shlibs
install -m0755 -d debian/libhts3/DEBIAN
echo "libhts 3 libhts3 (>= 1.18+ds)" >> debian/libhts3/DEBIAN/shlibs
chmod 0644 -- debian/libhts3/DEBIAN/shlibs
dpkg-gensymbols -plibhts3 -Idebian/libhts3.symbols -Pdebian/libhts3 -edebian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.18
mv debian/.debhelper/generated/libhts3/triggers.new debian/.debhelper/generated/libhts3/triggers
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/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix
install -m0755 -d debian/libhts3/DEBIAN
dpkg-shlibdeps -Tdebian/libhts3.substvars debian/libhts3/usr/lib/arm-linux-gnueabihf/libhts.so.1.18 debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
install -m0755 -d debian/libhts3/DEBIAN
install -p -m0644 debian/.debhelper/generated/libhts3/triggers debian/libhts3/DEBIAN/triggers
install -m0755 -d debian/libhts-dev/DEBIAN
install -m0755 -d debian/tabix/DEBIAN
dh_gencontrol -a
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 -Pdebian/libhts-dev
install -m0755 -d debian/libhts3/DEBIAN
echo misc:Depends= >> debian/libhts3.substvars
echo misc:Pre-Depends= >> debian/libhts3.substvars
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN
dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/.debhelper/libhts3/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libhts3-dbgsym "-DDepends=libhts3 (= \${binary:Version})" "-DDescription=debug symbols for libhts3" "-DBuild-Ids=5f0254dd32344e320e1295109d40ca7d31294722 96aa74da074b850c7fdd2a3d2fcf73fe4d7a6e3e bf4c199c52d746c4d0972628111833e07797e181 ec6ba8bcdf4a95d6908fb26f1c04bb659cb4225f f209f78e63f8581c3c029aec9a5737caa92c5dfb" -DSection=debug -UReplaces -UBreaks
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 -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=0f07c02d75ea01e2dc6da27f18ffaf0dbc7f5047 33216e1cfffb3239b20682337e4852751b240a02 ca8fa30bd452c7260014025acb52bf08ca3458ac" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
chmod 0644 -- debian/libhts-dev/DEBIAN/control
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/control
dpkg-gencontrol -plibhts3 -ldebian/changelog -Tdebian/libhts3.substvars -Pdebian/libhts3
chmod 0644 -- debian/tabix/DEBIAN/control
chmod 0644 -- debian/libhts3/DEBIAN/control
dh_md5sums -a
install -m0755 -d debian/libhts3/DEBIAN
install -m0755 -d debian/libhts-dev/DEBIAN
install -m0755 -d debian/tabix/DEBIAN
cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/libhts3 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/libhts3/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/libhts3/dbgsym-root/DEBIAN
cd debian/.debhelper/libhts3/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > 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/libhts-dev/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/libhts3/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a
dpkg-deb --root-owner-group --build debian/libhts3 ..
dpkg-deb --root-owner-group --build debian/libhts-dev ..
dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root ..
dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.18+ds-1_armhf.deb'.
dpkg-deb: building package 'libhts3' in '../libhts3_1.18+ds-1_armhf.deb'.
dpkg-deb: building package 'tabix-dbgsym' in '../tabix-dbgsym_1.18+ds-1_armhf.deb'.
dpkg-deb --root-owner-group --build debian/.debhelper/libhts3/dbgsym-root ..
dpkg-deb: building package 'libhts3-dbgsym' in '../libhts3-dbgsym_1.18+ds-1_armhf.deb'.
dpkg-deb --root-owner-group --build debian/tabix ..
dpkg-deb: building package 'tabix' in '../tabix_1.18+ds-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../htslib_1.18+ds-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../htslib_1.18+ds-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from htslib-1.18+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-11-10T05:27:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
htslib_1.18+ds-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 07 Nov 2023 19:46:30 +0100
Source: htslib
Binary: libhts-dev libhts3 libhts3-dbgsym tabix tabix-dbgsym
Architecture: armhf
Version: 1.18+ds-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
libhts-dev - development files for the HTSlib
libhts3 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Changes:
htslib (1.18+ds-1) unstable; urgency=medium
.
* Migrate htslib 1.18 from experimental to unstable.
Checksums-Sha1:
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Files:
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05ff5a26555d9b8232375439e2fd3dd3 1538520 libdevel optional libhts-dev_1.18+ds-1_armhf.deb
af217635d2a277a58373b964f95dd58c 1198364 debug optional libhts3-dbgsym_1.18+ds-1_armhf.deb
e1269246bfbf9250f02168d5dec11516 380028 libs optional libhts3_1.18+ds-1_armhf.deb
d789acdf6dfd36b65ea709bf66b94fb7 2586280 debug optional tabix-dbgsym_1.18+ds-1_armhf.deb
562070a4b856cd98f21245e939f10c6a 379520 science optional tabix_1.18+ds-1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: htslib
Binary: libhts-dev libhts3 libhts3-dbgsym tabix tabix-dbgsym
Architecture: armhf
Version: 1.18+ds-1
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Fri, 10 Nov 2023 05:27:11 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-13),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.2),
bash (= 5.2.15-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.2-5),
bsdutils (= 1:2.39.2-5),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-10+rpi1),
cpp-13 (= 13.2.0-5+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.7),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-5+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-10+rpi1),
gcc-12-base (= 12.3.0-10+rpi1),
gcc-13 (= 13.2.0-5+rpi1),
gcc-13-base (= 13.2.0-5+rpi1),
gettext (= 0.21-13),
gettext-base (= 0.21-13),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.65.2),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-5+rpi1),
libatomic1 (= 13.2.0-5+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.1-1),
libaudit1 (= 1:3.1.1-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.2-5),
libbrotli1 (= 1.0.9-2+b3),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcap-ng0 (= 0.8.3-1+b1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-5+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl3-gnutls (= 8.4.0-2+rpi1),
libcurl4-gnutls-dev (= 8.4.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg2-2),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.7),
libdeflate-dev (= 1.18-1),
libdeflate0 (= 1.18-1),
libdpkg-perl (= 1.22.1+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libffi8 (= 3.4.4-1),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-10+rpi1),
libgcc-13-dev (= 13.2.0-5+rpi1),
libgcc-s1 (= 13.2.0-5+rpi1),
libgcrypt20 (= 1.10.2-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.1-4),
libgomp1 (= 13.2.0-5+rpi1),
libgpg-error0 (= 1.47-2),
libgssapi-krb5-2 (= 1.20.1-4),
libhogweed6 (= 3.9.1-2),
libhtscodecs-dev (= 1.5.2-1),
libhtscodecs2 (= 1.5.2-1),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libk5crypto3 (= 1.20.1-4),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-4),
libkrb5support0 (= 1.20.1-4),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.4-0.1),
liblzma5 (= 5.4.4-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.2-5),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.58.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.25.0-5),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-9),
libpipeline1 (= 1.5.7-1),
libpsl5 (= 0.21.2-1+b1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-3),
libsasl2-modules-db (= 2.1.28+dfsg1-3),
libseccomp2 (= 2.5.4-1+rpi1+b1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.2-5),
libssh2-1 (= 1.11.0-2),
libssl-dev (= 3.0.11-1),
libssl3 (= 3.0.11-1),
libstdc++-13-dev (= 13.2.0-5+rpi1),
libstdc++6 (= 13.2.0-5+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 254.5-1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtinfo6 (= 6.4+20231016-1),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-5+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.2-5),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.11.2-3),
mawk (= 1.3.4.20230808-1),
ncurses-base (= 6.4+20231016-1),
ncurses-bin (= 6.4+20231016-1),
patch (= 2.7.6-7),
perl (= 5.36.0-9),
perl-base (= 5.36.0-9),
perl-modules-5.36 (= 5.36.0-9),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-3),
tar (= 1.34+dfsg-1.2),
usr-is-merged (= 37),
util-linux (= 2.39.2-5),
xz-utils (= 5.4.4-0.1),
zlib1g (= 1:1.2.13.dfsg-3),
zlib1g-dev (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1699382790"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libhts-dev_1.18+ds-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 1538520 bytes: control archive=1984 bytes.
1213 bytes, 27 lines control
2353 bytes, 36 lines md5sums
Package: libhts-dev
Source: htslib
Version: 1.18+ds-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4781
Depends: libhts3 (= 1.18+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.
.
For compatibility with sambamba, the internal routine cram_to_bam was
exported, hereto adopting a patch found in guix.
drwxr-xr-x root/root 0 2023-11-07 18:46 ./
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/include/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/include/htslib/
-rw-r--r-- root/root 16469 2023-07-20 15:01 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root 22175 2023-01-20 10:05 ./usr/include/htslib/cram.h
-rw-r--r-- root/root 15122 2023-07-20 15:01 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root 13351 2022-07-27 10:31 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root 57362 2023-07-25 08:16 ./usr/include/htslib/hts.h
-rw-r--r-- root/root 4010 2021-10-15 15:03 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root 11708 2022-08-12 11:26 ./usr/include/htslib/hts_endian.h
-rw-r--r-- root/root 5991 2022-07-14 09:33 ./usr/include/htslib/hts_expr.h
-rw-r--r-- root/root 3958 2022-05-13 15:25 ./usr/include/htslib/hts_log.h
-rw-r--r-- root/root 2842 2022-01-11 12:11 ./usr/include/htslib/hts_os.h
-rw-r--r-- root/root 5605 2020-01-23 10:28 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root 2828 2019-11-19 11:20 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root 22903 2023-04-06 07:36 ./usr/include/htslib/khash.h
-rw-r--r-- root/root 4050 2020-08-10 08:46 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root 5135 2019-11-19 11:20 ./usr/include/htslib/klist.h
-rw-r--r-- root/root 3733 2022-07-27 10:31 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root 3295 2020-08-27 10:09 ./usr/include/htslib/kroundup.h
-rw-r--r-- root/root 9224 2023-07-20 15:01 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root 11507 2022-08-16 10:42 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root 11462 2022-07-27 10:31 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root 8881 2020-07-29 13:09 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root 91648 2023-06-30 14:25 ./usr/include/htslib/sam.h
-rw-r--r-- root/root 16584 2023-06-05 14:19 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root 4956 2022-05-13 15:25 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root 12747 2020-09-16 09:17 ./usr/include/htslib/thread_pool.h
-rw-r--r-- root/root 68420 2023-07-20 15:01 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root 1686 2020-07-11 11:34 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root 4919 2020-09-16 09:17 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 4373630 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/libhts.a
lrwxrwxrwx root/root 0 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.18
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 678 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root 2680 2021-04-12 09:37 ./usr/share/doc/libhts-dev/README
-rw-r--r-- root/root 2961 2019-12-10 17:59 ./usr/share/doc/libhts-dev/README.large_positions.md.gz
-rw-r--r-- root/root 401 2022-07-03 07:14 ./usr/share/doc/libhts-dev/README.test
-rw-r--r-- root/root 3127 2023-11-07 18:46 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root 33517 2023-07-25 08:16 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root 5897 2023-08-23 16:41 ./usr/share/doc/libhts-dev/copyright
libhts3-dbgsym_1.18+ds-1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 1198364 bytes: control archive=820 bytes.
555 bytes, 13 lines control
617 bytes, 6 lines md5sums
Package: libhts3-dbgsym
Source: htslib
Version: 1.18+ds-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1270
Depends: libhts3 (= 1.18+ds-1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libhts3
Build-Ids: 5f0254dd32344e320e1295109d40ca7d31294722 96aa74da074b850c7fdd2a3d2fcf73fe4d7a6e3e bf4c199c52d746c4d0972628111833e07797e181 ec6ba8bcdf4a95d6908fb26f1c04bb659cb4225f f209f78e63f8581c3c029aec9a5737caa92c5dfb
drwxr-xr-x root/root 0 2023-11-07 18:46 ./
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/5f/
-rw-r--r-- root/root 49164 2023-11-07 18:46 ./usr/lib/debug/.build-id/5f/0254dd32344e320e1295109d40ca7d31294722.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root 23112 2023-11-07 18:46 ./usr/lib/debug/.build-id/96/aa74da074b850c7fdd2a3d2fcf73fe4d7a6e3e.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 36196 2023-11-07 18:46 ./usr/lib/debug/.build-id/bf/4c199c52d746c4d0972628111833e07797e181.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/ec/
-rw-r--r-- root/root 1145932 2023-11-07 18:46 ./usr/lib/debug/.build-id/ec/6ba8bcdf4a95d6908fb26f1c04bb659cb4225f.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/f2/
-rw-r--r-- root/root 12936 2023-11-07 18:46 ./usr/lib/debug/.build-id/f2/09f78e63f8581c3c029aec9a5737caa92c5dfb.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 12448 2023-11-07 18:46 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-11-07 18:46 ./usr/share/doc/libhts3-dbgsym -> libhts3
libhts3_1.18+ds-1_armhf.deb
---------------------------
new Debian package, version 2.0.
size 380028 bytes: control archive=6024 bytes.
1221 bytes, 23 lines control
887 bytes, 12 lines md5sums
30 bytes, 1 lines shlibs
30122 bytes, 930 lines symbols
68 bytes, 2 lines triggers
Package: libhts3
Source: htslib
Version: 1.18+ds-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 945
Depends: libbz2-1.0, libc6 (>= 2.34), libcurl3-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), libssl3 (>= 3.0.0), zlib1g (>= 1:1.1.4)
Breaks: ivar (<< 1.3.1~), libhts-dev (<< 1.13~), libtabixpp (<< 1.0.0-5~), samtools (<< 1.17~)
Replaces: libhts-dev (<< 1.13~)
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 2023-11-07 18:46 ./
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/htslib/
-rw-r--r-- root/root 9660 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so
-rw-r--r-- root/root 26044 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so
-rw-r--r-- root/root 30188 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so
-rw-r--r-- root/root 13756 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so
-rw-r--r-- root/root 783908 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.18
lrwxrwxrwx root/root 0 2023-11-07 18:46 ./usr/lib/arm-linux-gnueabihf/libhts.so.3 -> libhts.so.1.18
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/libhts3/
-rw-r--r-- root/root 3127 2023-11-07 18:46 ./usr/share/doc/libhts3/changelog.Debian.gz
-rw-r--r-- root/root 33517 2023-07-25 08:16 ./usr/share/doc/libhts3/changelog.gz
-rw-r--r-- root/root 5897 2023-08-23 16:41 ./usr/share/doc/libhts3/copyright
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/man/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/man/man5/
-rw-r--r-- root/root 2452 2023-11-07 18:46 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root 1537 2023-11-07 18:46 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root 1857 2023-11-07 18:46 ./usr/share/man/man5/vcf.5.gz
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/man/man7/
-rw-r--r-- root/root 3416 2023-11-07 18:46 ./usr/share/man/man7/htslib-s3-plugin.7.gz
tabix-dbgsym_1.18+ds-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 2586280 bytes: control archive=700 bytes.
450 bytes, 12 lines control
403 bytes, 4 lines md5sums
Package: tabix-dbgsym
Source: htslib
Version: 1.18+ds-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2726
Depends: tabix (= 1.18+ds-1)
Section: debug
Priority: optional
Description: debug symbols for tabix
Build-Ids: 0f07c02d75ea01e2dc6da27f18ffaf0dbc7f5047 33216e1cfffb3239b20682337e4852751b240a02 ca8fa30bd452c7260014025acb52bf08ca3458ac
drwxr-xr-x root/root 0 2023-11-07 18:46 ./
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/0f/
-rw-r--r-- root/root 776664 2023-11-07 18:46 ./usr/lib/debug/.build-id/0f/07c02d75ea01e2dc6da27f18ffaf0dbc7f5047.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/33/
-rw-r--r-- root/root 948472 2023-11-07 18:46 ./usr/lib/debug/.build-id/33/216e1cfffb3239b20682337e4852751b240a02.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.build-id/ca/
-rw-r--r-- root/root 972868 2023-11-07 18:46 ./usr/lib/debug/.build-id/ca/8fa30bd452c7260014025acb52bf08ca3458ac.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 75972 2023-11-07 18:46 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-11-07 18:46 ./usr/share/doc/tabix-dbgsym -> tabix
tabix_1.18+ds-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 379520 bytes: control archive=1128 bytes.
985 bytes, 20 lines control
545 bytes, 9 lines md5sums
Package: tabix
Source: htslib
Version: 1.18+ds-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1907
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 2023-11-07 18:46 ./
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/bin/
-rwxr-xr-x root/root 550572 2023-11-07 18:46 ./usr/bin/bgzip
-rwxr-xr-x root/root 661176 2023-11-07 18:46 ./usr/bin/htsfile
-rwxr-xr-x root/root 677556 2023-11-07 18:46 ./usr/bin/tabix
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/doc/tabix/
-rw-r--r-- root/root 3127 2023-11-07 18:46 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root 33517 2023-07-25 08:16 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root 5897 2023-08-23 16:41 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/man/
drwxr-xr-x root/root 0 2023-11-07 18:46 ./usr/share/man/man1/
-rw-r--r-- root/root 2920 2023-11-07 18:46 ./usr/share/man/man1/bgzip.1.gz
-rw-r--r-- root/root 1916 2023-11-07 18:46 ./usr/share/man/man1/htsfile.1.gz
-rw-r--r-- root/root 3341 2023-11-07 18:46 ./usr/share/man/man1/tabix.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 63408
Build-Time: 101
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 20
Job: htslib_1.18+ds-1
Machine Architecture: arm64
Package: htslib
Package-Time: 130
Source-Version: 1.18+ds-1
Space: 63408
Status: successful
Version: 1.18+ds-1
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Finished at 2023-11-10T05:27:12Z
Build needed 00:02:10, 63408k disk space