[Debian-med-packaging] htslib_1.3.1-1~bpo8+1_source.changes REJECTED
Afif Elghraoui
afif at ghraoui.name
Sun May 8 21:15:55 UTC 2016
Hi, Charles,
I guess you ran out of time for the day to take care of this. I went
ahead and made the build and binary upload.
Knowing you like to keep track of the build logs, please find them
attached. :)
Thanks and regards
Afif
على الأحد 8 أيار 2016 06:19، كتب Debian FTP Masters:
>
>
> Uploads not including architecture-independent packages are not allowed.
>
> ===
>
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address our
> concerns.
>
>
> _______________________________________________
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>
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
-------------- next part --------------
sbuild (Debian sbuild) 0.68.0 (15 Jan 2016) on afif-1215B
+==============================================================================+
| htslib 1.3.1-1~bpo8+1 (amd64) 08 May 2016 13:54 |
+==============================================================================+
Package: htslib
Version: 1.3.1-1~bpo8+1
Source Version: 1.3.1-1~bpo8+1
Distribution: jessie-backports
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
I: NOTICE: Log filtering will replace 'build/htslib-aHK0ED/htslib-1.3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/htslib-aHK0ED' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-amd64-sbuild-f5a3f6b6-de37-46ec-b4fd-b7d7e351aa9b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Ign http://ftp.us.debian.org jessie InRelease
Hit http://ftp.us.debian.org jessie Release.gpg
Hit http://ftp.us.debian.org jessie Release
Hit http://ftp.us.debian.org jessie/main Sources
Hit http://ftp.us.debian.org jessie/main amd64 Packages
Hit http://ftp.us.debian.org jessie/main Translation-en
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0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Local sources
-------------
/home/afif/مشاريع/debian/med/htslib/htslib_1.3.1-1~bpo8+1.dsc exists in /home/afif/مشاريع/debian/med/htslib; copying to chroot
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/<<BUILDDIR>>/resolver-YX_a4L/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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Ign file: ./ Translation-en
Reading package lists...
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Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
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+------------------------------------------------------------------------------+
| Check architectures |
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Arch check ok (amd64 included in any all)
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| Install package build dependencies |
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Setup apt archive
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Merged Build-Depends: debhelper (>= 9), dh-exec, libcurl4-gnutls-dev, libssl-dev, zlib1g-dev, autoconf
Filtered Build-Depends: debhelper (>= 9), dh-exec, libcurl4-gnutls-dev, libssl-dev, zlib1g-dev, autoconf
dpkg-deb: building package `sbuild-build-depends-htslib-dummy' in `/<<BUILDDIR>>/resolver-mGXQsc/apt_archive/sbuild-build-depends-htslib-dummy.deb'.
OK
Ign file: ./ InRelease
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Ign file: ./ Translation-en
Reading package lists...
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Install htslib build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
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Reading state information...
The following extra packages will be installed:
autoconf bsdmainutils debhelper dh-exec file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev
libffi6 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libidn11
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1
libnettle4 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db
libsigsegv2 libssh2-1 libssl-dev libssl1.0.0 libtasn1-6 libunistring0
libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc libtool wamerican wordlist whois
vacation dh-make gettext-doc groff libcurl4-doc libcurl3-dbg libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config
gnutls-bin krb5-doc krb5-user less www-browser libmail-box-perl
Recommended packages:
automake automaken curl wget lynx-cur autopoint libasprintf-dev
libgettextpo-dev ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libsasl2-modules libssl-doc xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf bsdmainutils debhelper dh-exec file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev
libffi6 libglib2.0-0 libgnutls-deb0-28 libgssapi-krb5-2 libhogweed2 libidn11
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1
libnettle4 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db
libsigsegv2 libssh2-1 libssl-dev libssl1.0.0 libtasn1-6 libunistring0
libxml2 m4 man-db po-debconf sbuild-build-depends-htslib-dummy zlib1g-dev
0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded.
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Get:18 http://ftp.us.debian.org/debian/ jessie/main libidn11 amd64 1.29-1+b2 [136 kB]
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Get:30 http://ftp.us.debian.org/debian/ jessie/main libunistring0 amd64 0.9.3-5.2+b1 [288 kB]
Get:31 http://ftp.us.debian.org/debian/ jessie/main file amd64 1:5.22+15-2+deb8u1 [60.4 kB]
Get:32 http://ftp.us.debian.org/debian/ jessie/main gettext-base amd64 0.19.3-2 [121 kB]
Get:33 http://ftp.us.debian.org/debian/ jessie/main m4 amd64 1.4.17-4 [254 kB]
Get:34 http://ftp.us.debian.org/debian/ jessie/main autoconf all 2.69-8 [340 kB]
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Get:36 http://ftp.us.debian.org/debian/ jessie/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:37 http://ftp.us.debian.org/debian/ jessie/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:38 http://ftp.us.debian.org/debian/ jessie/main debhelper all 9.20150101 [813 kB]
Get:39 http://ftp.us.debian.org/debian/ jessie/main libcurl4-gnutls-dev amd64 7.38.0-4+deb8u3 [327 kB]
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Get:41 http://ftp.us.debian.org/debian/ jessie/main libssl-dev amd64 1.0.1k-3+deb8u4 [1273 kB]
Get:42 http://ftp.us.debian.org/debian/ jessie/main dh-exec amd64 0.14 [23.6 kB]
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Setting up libp11-kit0:amd64 (0.20.7-1) ...
Setting up libtasn1-6:amd64 (4.2-3+deb8u1) ...
Setting up libgnutls-deb0-28:amd64 (3.3.8-6+deb8u3) ...
Setting up libkeyutils1:amd64 (1.5.9-5+b1) ...
Setting up libkrb5support0:amd64 (1.12.1+dfsg-19+deb8u2) ...
Setting up libk5crypto3:amd64 (1.12.1+dfsg-19+deb8u2) ...
Setting up libkrb5-3:amd64 (1.12.1+dfsg-19+deb8u2) ...
Setting up libgssapi-krb5-2:amd64 (1.12.1+dfsg-19+deb8u2) ...
Setting up libidn11:amd64 (1.29-1+b2) ...
Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-13+deb8u1) ...
Setting up libsasl2-2:amd64 (2.1.26.dfsg1-13+deb8u1) ...
Setting up libldap-2.4-2:amd64 (2.4.40+dfsg-1+deb8u2) ...
Setting up libmagic1:amd64 (1:5.22+15-2+deb8u1) ...
Setting up libxml2:amd64 (2.9.1+dfsg1-5+deb8u1) ...
Setting up libglib2.0-0:amd64 (2.42.1-1+b1) ...
No schema files found: doing nothing.
Setting up libcroco3:amd64 (0.6.8-3+b1) ...
Setting up librtmp1:amd64 (2.4+20150115.gita107cef-1) ...
Setting up libssh2-1:amd64 (1.4.3-4.1+deb8u1) ...
Setting up libcurl3-gnutls:amd64 (7.38.0-4+deb8u3) ...
Setting up libsigsegv2:amd64 (2.10-4+b1) ...
Setting up libunistring0:amd64 (0.9.3-5.2+b1) ...
Setting up file (1:5.22+15-2+deb8u1) ...
Setting up gettext-base (0.19.3-2) ...
Setting up m4 (1.4.17-4) ...
Setting up autoconf (2.69-8) ...
Setting up gettext (0.19.3-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu3) ...
Setting up debhelper (9.20150101) ...
Setting up libcurl4-gnutls-dev:amd64 (7.38.0-4+deb8u3) ...
Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
Setting up libssl-dev:amd64 (1.0.1k-3+deb8u4) ...
Setting up dh-exec (0.14) ...
Setting up sbuild-build-depends-htslib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18+deb8u4) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.26 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18+deb8u4 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt25-1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8.3 autoconf_2.69-8 base-files_8+deb8u4 base-passwd_3.5.37 bash_4.3-11+b1 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7+b3 coreutils_8.23-4 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4+b1 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150101 debian-archive-keyring_2014.3 debianutils_4.4+b1 dh-exec_0.14 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-2.2 dpkg_1.17.26 dpkg-dev_1.17.26 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2+deb8u1 findutils_4.4.2-9+b1 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.3-2 gettext-base_0.19.3-2 gnupg_1.4.18-7+deb8u1 gpgv_1.4.18-7+deb8u1 grep_2.20-4.1 groff-base_1.22.2-8 gzip_1.6-4 hostname_3.15 init_1.22 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8.3 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1+b1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7+b3 libc-bin_2.19-18+deb8u4 libc-dev-bin_2.19-18+deb8u4 libc6_2.19-18+deb8u4 libc6-dev_2.19-18+deb8u4 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcilkrts5_4.9.2-10 libcloog-isl4_0.18.2-1+b2 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3+b1 libcryptsetup4_2:1.6.6-5 libcurl3-gnutls_7.38.0-4+deb8u3 libcurl4-gnutls-dev_7.38.0-4+deb8u3 libdb5.3_5.3.28-9 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.26 libfakeroot_1.20.2-1 libffi6_3.1-2+b2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2+deb8u1 libgdbm3_1.8.3-13.1 libglib2.0-0_2.42.1-1+b1 libgmp10_2:6.0.0+dfsg-6 libgnutls-deb0-28_3.3.8-6+deb8u3 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libgssapi-krb5-2_1.12.1+dfsg-19+deb8u2 libhogweed2_2.7.1-5+deb8u1 libidn11_1.29-1+b2 libisl10_0.12.2-2 libitm1_4.9.2-10 libk5crypto3_1.12.1+dfsg-19+deb8u2 libkeyutils1_1.5.9-5+b1 libkmod2_18-3 libkrb5-3_1.12.1+dfsg-19+deb8u2 libkrb5support0_1.12.1+dfsg-19+deb8u2 libldap-2.4-2_2.4.40+dfsg-1+deb8u2 liblocale-gettext-perl_1.05-8+b1 liblsan0_4.9.2-10 liblzma5_5.1.1alpha+20120614-2+b3 libmagic1_1:5.22+15-2+deb8u1 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1+b1 libncursesw5_5.9+20140913-1+b1 libnettle4_2.7.1-5+deb8u1 libp11-kit0_0.20.7-1 libpam-modules_1.1.8-3.1+deb8u1+b1 libpam-modules-bin_1.1.8-3.1+deb8u1+b1 libpam-runtime_1.1.8-3.1+deb8u1 libpam0g_1.1.8-3.1+deb8u1+b1 libpcre3_2:8.35-3.3+deb8u4 libpipeline1_1.4.0-1 libprocps3_2:3.3.9-9 libquadmath0_4.9.2-10 libreadline6_6.3-8+b3 librtmp1_2.4+20150115.gita107cef-1 libsasl2-2_2.1.26.dfsg1-13+deb8u1 libsasl2-modules-db_2.1.26.dfsg1-13+deb8u1 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1+b1 libsepol1_2.3-2 libsigsegv2_2.10-4+b1 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libss2_1.42.12-1.1 libssh2-1_1.4.3-4.1+deb8u1 libssl-dev_1.0.1k-3+deb8u4 libssl1.0.0_1.0.1k-3+deb8u4 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17+deb8u4 libtasn1-6_4.2-3+deb8u1 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1+b1 libtsan0_4.9.2-10 libubsan0_4.9.2-10 libudev1_215-17+deb8u4 libunistring0_0.9.3-5.2+b1 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3+b2 libuuid1_2.25.2-6 libxml2_2.9.1+dfsg1-5+deb8u1 linux-libc-dev_3.16.7-ckt25-1 login_1:4.2-3+deb8u1 lsb-base_4.1+Debian13+nmu1 m4_1.4.17-4 make_4.0-8.1 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 multiarch-support_2.19-18+deb8u4 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1+b1 passwd_1:4.2-3+deb8u1 patch_2.7.5-1 perl_5.20.2-3+deb8u4 perl-base_5.20.2-3+deb8u4 perl-modules_5.20.2-3+deb8u4 po-debconf_1.0.16+nmu3 procps_2:3.3.9-9 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-htslib-dummy_0.invalid.0 sed_4.2.2-4+b1 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17+deb8u4 systemd-sysv_215-17+deb8u4 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2+b1 tzdata_2016c-0+deb8u1 udev_215-17+deb8u4 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2+b3 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
dpkg-source: warning: extracting unsigned source package (htslib_1.3.1-1~bpo8+1.dsc)
dpkg-source: info: extracting htslib in htslib-1.3.1
dpkg-source: info: unpacking htslib_1.3.1.orig.tar.gz
dpkg-source: info: unpacking htslib_1.3.1-1~bpo8+1.debian.tar.xz
dpkg-source: info: applying define_PATH_MAX.patch
dpkg-source: info: applying literal_version.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=afif
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=jessie-amd64-sbuild
SCHROOT_CHROOT_NAME=jessie-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=afif
SCHROOT_SESSION_ID=jessie-amd64-sbuild-f5a3f6b6-de37-46ec-b4fd-b7d7e351aa9b
SCHROOT_UID=1000
SCHROOT_USER=afif
SHELL=/bin/sh
TERM=xterm
USER=afif
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
XDG_SESSION_ID=1
XDG_VTNR=7
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package htslib
dpkg-buildpackage: source version 1.3.1-1~bpo8+1
dpkg-buildpackage: source distribution jessie-backports
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build htslib-1.3.1
dpkg-buildpackage: host architecture amd64
dpkg-source: info: using options from htslib-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
make -j2 distclean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.*
rm -f libhts.so libhts.so.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.a bgzip htsfile tabix test/fieldarith test/hfile test/sam test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS *-uninstalled.pc
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean -O--parallel
rm -f debian/libhts1.substvars
rm -f debian/libhts1.*.debhelper
rm -rf debian/libhts1/
rm -f debian/libhts-dev.substvars
rm -f debian/libhts-dev.*.debhelper
rm -rf debian/libhts-dev/
rm -f debian/htslib-test.substvars
rm -f debian/htslib-test.*.debhelper
rm -rf debian/htslib-test/
rm -f debian/tabix.substvars
rm -f debian/tabix.*.debhelper
rm -rf debian/tabix/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -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 \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *-stamp
dpkg-source -b htslib-1.3.1
dpkg-source: info: using options from htslib-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building htslib using existing ./htslib_1.3.1.orig.tar.gz
dpkg-source: info: building htslib in htslib_1.3.1-1~bpo8+1.debian.tar.xz
dpkg-source: info: building htslib in htslib_1.3.1-1~bpo8+1.dsc
debian/rules build
dh build --parallel
dh_testdir -O--parallel
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
autoconf
./configure --enable-libcurl
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
# re-try later LDLIBS=-lhts \
PACKAGE_VERSION="1.3.1-1~bpo8+1" \
libdir=/usr/lib/x86_64-linux-gnu
make -j2 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kfunc.o kfunc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o knetfile.o knetfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o kstring.o kstring.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o bgzf.o bgzf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile.o hfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3.1"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o md5.o md5.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o tbx.o tbx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/files.o cram/files.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/vlen.o cram/vlen.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o cram/zfio.o cram/zfio.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hfile_libcurl.o hfile_libcurl.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kfunc.pico kfunc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o knetfile.pico knetfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o kstring.pico kstring.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o bgzf.pico bgzf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o faidx.pico faidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile.pico hfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hts.pico hts.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o md5.pico md5.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o regidx.pico regidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o sam.pico sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o tbx.pico tbx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcf.pico vcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/files.pico cram/files.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/vlen.pico cram/vlen.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o cram/zfio.pico cram/zfio.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -fpic -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o bgzip.o bgzip.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o htsfile.o htsfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/fieldarith.o test/fieldarith.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/hfile.o test/hfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/sam.o test/sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test_view.o test/test_view.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -DSAMTOOLS=1 -D_FORTIFY_SOURCE=2 -c -o hts.o hts.c
gcc -shared -Wl,-soname,libhts.so.1 -pthread -Wl,-z,relro -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.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_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico hfile_libcurl.pico -lz -lm -lcurl -lcrypto
ln -sf libhts.so libhts.so.1
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o hfile_libcurl.o
ranlib libhts.a
gcc -pthread -Wl,-z,relro -o bgzip bgzip.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o htsfile htsfile.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o tabix tabix.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o test/fieldarith test/fieldarith.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o test/hfile test/hfile.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o test/sam test/sam.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o test/test-regidx test/test-regidx.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o test/test_view test/test_view.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lcurl -lcrypto
gcc -pthread -Wl,-z,relro -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lcurl -lcrypto
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test
make -j2 test
make[2]: Entering directory '/<<PKGBUILDDIR>>'
test/fieldarith test/fieldarith.sam
test/hfile
test/sam test/ce.fa test/faidx.fa
test/test-regidx
cd test && REF_PATH=: ./test.pl
test_view testing auxf#values.sam, ref auxf.fa:
./test_view -S -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 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 auxf#values.tmp.bam > auxf#values.tmp.bam.cram
./test_view -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -t auxf.fa -S -C -o VERSION=3.0 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 -b -D auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam
./test_view auxf#values.tmp.bam.cram.bam > auxf#values.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_
./test_view -t auxf.fa -C -o VERSION=2.1 auxf#values.tmp.cram > auxf#values.tmp.cram.cram
./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.cram.cram > auxf#values.tmp.cram
./test_view auxf#values.tmp.cram > auxf#values.tmp.cram.sam_
./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_
.. ok
test_view testing c1#bounds.sam, ref c1.fa:
./test_view -S -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 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 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram
./test_view -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 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 -b -D c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam
./test_view c1#bounds.tmp.bam.cram.bam > c1#bounds.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#bounds.tmp.cram > c1#bounds.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.cram.cram > c1#bounds.tmp.cram
./test_view c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_
./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_
.. ok
test_view testing c1#clip.sam, ref c1.fa:
./test_view -S -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 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 c1#clip.tmp.bam > c1#clip.tmp.bam.cram
./test_view -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 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 -b -D c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam
./test_view c1#clip.tmp.bam.cram.bam > c1#clip.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#clip.tmp.cram > c1#clip.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.cram.cram > c1#clip.tmp.cram
./test_view c1#clip.tmp.cram > c1#clip.tmp.cram.sam_
./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_
.. ok
test_view testing c1#noseq.sam, ref c1.fa:
./test_view -S -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 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 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram
./test_view -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 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 -b -D c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam
./test_view c1#noseq.tmp.bam.cram.bam > c1#noseq.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#noseq.tmp.cram > c1#noseq.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.cram.cram > c1#noseq.tmp.cram
./test_view c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_
./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_
.. ok
test_view testing c1#pad1.sam, ref c1.fa:
./test_view -S -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 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 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram
./test_view -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 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 -b -D c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam
./test_view c1#pad1.tmp.bam.cram.bam > c1#pad1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad1.tmp.cram > c1#pad1.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.cram.cram > c1#pad1.tmp.cram
./test_view c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_
.. ok
test_view testing c1#pad2.sam, ref c1.fa:
./test_view -S -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 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 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram
./test_view -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 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 -b -D c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam
./test_view c1#pad2.tmp.bam.cram.bam > c1#pad2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad2.tmp.cram > c1#pad2.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.cram.cram > c1#pad2.tmp.cram
./test_view c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_
./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_
.. ok
test_view testing c1#pad3.sam, ref c1.fa:
./test_view -S -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 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 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram
./test_view -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 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 -b -D c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam
./test_view c1#pad3.tmp.bam.cram.bam > c1#pad3.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#pad3.tmp.cram > c1#pad3.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.cram.cram > c1#pad3.tmp.cram
./test_view 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 -S -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 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 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram
./test_view -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -S -C -o VERSION=3.0 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 -b -D c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam
./test_view c1#unknown.tmp.bam.cram.bam > c1#unknown.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_
./test_view -t c1.fa -C -o VERSION=2.1 c1#unknown.tmp.cram > c1#unknown.tmp.cram.cram
./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.cram.cram > c1#unknown.tmp.cram
./test_view c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_
./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_
.. ok
test_view testing c2#pad.sam, ref c2.fa:
./test_view -S -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 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 c2#pad.tmp.bam > c2#pad.tmp.bam.cram
./test_view -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -t c2.fa -S -C -o VERSION=3.0 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 -b -D c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam
./test_view c2#pad.tmp.bam.cram.bam > c2#pad.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_
./test_view -t c2.fa -C -o VERSION=2.1 c2#pad.tmp.cram > c2#pad.tmp.cram.cram
./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.cram.cram > c2#pad.tmp.cram
./test_view c2#pad.tmp.cram > c2#pad.tmp.cram.sam_
./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_
.. ok
test_view testing ce#1.sam, ref ce.fa:
./test_view -S -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 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 ce#1.tmp.bam > ce#1.tmp.bam.cram
./test_view -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam
./test_view ce#1.tmp.bam.cram.bam > ce#1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#1.tmp.cram > ce#1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.cram.cram > ce#1.tmp.cram
./test_view ce#1.tmp.cram > ce#1.tmp.cram.sam_
./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_
.. ok
test_view testing ce#2.sam, ref ce.fa:
./test_view -S -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 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 ce#2.tmp.bam > ce#2.tmp.bam.cram
./test_view -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam
./test_view ce#2.tmp.bam.cram.bam > ce#2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#2.tmp.cram > ce#2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.cram.cram > ce#2.tmp.cram
./test_view ce#2.tmp.cram > ce#2.tmp.cram.sam_
./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_
.. ok
test_view testing ce#5.sam, ref ce.fa:
./test_view -S -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 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 ce#5.tmp.bam > ce#5.tmp.bam.cram
./test_view -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam
./test_view ce#5.tmp.bam.cram.bam > ce#5.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#5.tmp.cram > ce#5.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.cram.cram > ce#5.tmp.cram
./test_view 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 -S -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 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 ce#5b.tmp.bam > ce#5b.tmp.bam.cram
./test_view -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam
./test_view ce#5b.tmp.bam.cram.bam > ce#5b.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#5b.tmp.cram > ce#5b.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.cram.cram > ce#5b.tmp.cram
./test_view ce#5b.tmp.cram > ce#5b.tmp.cram.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_
./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_
./compare_sam.pl -nomd ce#5b.sam ce#5b_java.tmp.sam_
.. ok
test_view testing ce#large_seq.sam, ref ce.fa:
./test_view -S -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 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 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram
./test_view -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view ce#large_seq.tmp.bam.cram.bam > 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 -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam
./test_view ce#large_seq.tmp.bam.cram.bam > 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 -t ce.fa -C -o VERSION=2.1 ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.cram.cram > ce#large_seq.tmp.cram
./test_view 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 -S -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 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 ce#supp.tmp.bam > ce#supp.tmp.bam.cram
./test_view -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam
./test_view ce#supp.tmp.bam.cram.bam > ce#supp.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#supp.tmp.cram > ce#supp.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.cram.cram > ce#supp.tmp.cram
./test_view 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 -S -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 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 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram
./test_view -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam
./test_view ce#tag_depadded.tmp.bam.cram.bam > ce#tag_depadded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.cram.cram > ce#tag_depadded.tmp.cram
./test_view 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_
.. ok
test_view testing ce#tag_padded.sam, ref ce.fa:
./test_view -S -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 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 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram
./test_view -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam
./test_view ce#tag_padded.tmp.bam.cram.bam > ce#tag_padded.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.cram.cram > ce#tag_padded.tmp.cram
./test_view 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_
.. ok
test_view testing ce#unmap.sam, ref ce.fa:
./test_view -S -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 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 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram
./test_view -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam
./test_view ce#unmap.tmp.bam.cram.bam > ce#unmap.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap.tmp.cram > ce#unmap.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.cram.cram > ce#unmap.tmp.cram
./test_view ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_
.. ok
test_view testing ce#unmap1.sam, ref ce.fa:
./test_view -S -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 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 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram
./test_view -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam
./test_view ce#unmap1.tmp.bam.cram.bam > ce#unmap1.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.cram.cram > ce#unmap1.tmp.cram
./test_view ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_
.. ok
test_view testing ce#unmap2.sam, ref ce.fa:
./test_view -S -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 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 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram
./test_view -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -S -C -o VERSION=3.0 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 -b -D ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam
./test_view ce#unmap2.tmp.bam.cram.bam > ce#unmap2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_
./test_view -t ce.fa -C -o VERSION=2.1 ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.cram
./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.cram.cram > ce#unmap2.tmp.cram
./test_view ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_
./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_
.. ok
test_view testing xx#blank.sam, ref xx.fa:
./test_view -S -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 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 xx#blank.tmp.bam > xx#blank.tmp.bam.cram
./test_view -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam
./test_view xx#blank.tmp.bam.cram.bam > xx#blank.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#blank.tmp.cram > xx#blank.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.cram.cram > xx#blank.tmp.cram
./test_view 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 -S -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 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 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram
./test_view -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view xx#large_aux.tmp.bam.cram.bam > 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 -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam
./test_view xx#large_aux.tmp.bam.cram.bam > 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 -t xx.fa -C -o VERSION=2.1 xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.cram.cram > xx#large_aux.tmp.cram
./test_view 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 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_
WARNING: Header @SQ length mismatch for ref xx, 30 vs 20
./compare_sam.pl -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 -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 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 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram
./test_view -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam
./test_view xx#large_aux2.tmp.bam.cram.bam > xx#large_aux2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.cram.cram > xx#large_aux2.tmp.cram
./test_view 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_
.. ok
test_view testing xx#minimal.sam, ref xx.fa:
./test_view -S -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 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 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram
./test_view -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam
./test_view xx#minimal.tmp.bam.cram.bam > xx#minimal.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#minimal.tmp.cram > xx#minimal.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.cram.cram > xx#minimal.tmp.cram
./test_view xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_
./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_
.. ok
test_view testing xx#pair.sam, ref xx.fa:
./test_view -S -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 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 xx#pair.tmp.bam > xx#pair.tmp.bam.cram
./test_view -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam
./test_view xx#pair.tmp.bam.cram.bam > xx#pair.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#pair.tmp.cram > xx#pair.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.cram.cram > xx#pair.tmp.cram
./test_view 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 -S -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 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 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram
./test_view -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam
./test_view xx#repeated.tmp.bam.cram.bam > xx#repeated.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#repeated.tmp.cram > xx#repeated.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.cram.cram > xx#repeated.tmp.cram
./test_view xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_
./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_
.. ok
test_view testing xx#rg.sam, ref xx.fa:
./test_view -S -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 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 xx#rg.tmp.bam > xx#rg.tmp.bam.cram
./test_view -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam
./test_view xx#rg.tmp.bam.cram.bam > xx#rg.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#rg.tmp.cram > xx#rg.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.cram.cram > xx#rg.tmp.cram
./test_view xx#rg.tmp.cram > xx#rg.tmp.cram.sam_
./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_
.. ok
test_view testing xx#tlen.sam, ref xx.fa:
./test_view -S -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 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 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram
./test_view -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam
./test_view xx#tlen.tmp.bam.cram.bam > xx#tlen.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen.tmp.cram > xx#tlen.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.cram.cram > xx#tlen.tmp.cram
./test_view 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 -S -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 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 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram
./test_view -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam
./test_view xx#tlen2.tmp.bam.cram.bam > xx#tlen2.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.cram.cram > xx#tlen2.tmp.cram
./test_view xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_
./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_
.. ok
test_view testing xx#triplet.sam, ref xx.fa:
./test_view -S -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 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 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram
./test_view -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam
./test_view xx#triplet.tmp.bam.cram.bam > xx#triplet.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#triplet.tmp.cram > xx#triplet.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.cram.cram > xx#triplet.tmp.cram
./test_view xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_
./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_
.. ok
test_view testing xx#unsorted.sam, ref xx.fa:
./test_view -S -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 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 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram
./test_view -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -S -C -o VERSION=3.0 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 -b -D xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam
./test_view xx#unsorted.tmp.bam.cram.bam > xx#unsorted.tmp.bam.cram.bam.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_
./test_view -t xx.fa -C -o VERSION=2.1 xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.cram
./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.cram.cram > xx#unsorted.tmp.cram
./test_view xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_
./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_
.. ok
test_vcf_api:
/<<PKGBUILDDIR>>/test/test-vcf-api /tmp/xLOo4Mo2HC/test-vcf-api.bcf
.. ok
test_vcf_sweep:
/<<PKGBUILDDIR>>/test/test-vcf-sweep /tmp/xLOo4Mo2HC/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_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/xLOo4Mo2HC/headernul0.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/xLOo4Mo2HC/headernul1.bam
.. ok
test_convert_padded_header:
/<<PKGBUILDDIR>>/test/test_view -t ce.fa -C /tmp/xLOo4Mo2HC/headernul678.bam
.. ok
Number of tests:
total .. 39
passed .. 39
failed .. 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f test/*.tmp test/*.tmp.* test/*.o test/*.dSYM \
test/fieldarith test/hfile test/test_view test/test-vcf-api test/test-vcf-sweep
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary
dh binary --parallel
dh_testroot -O--parallel
dh_prep -O--parallel
rm -f debian/libhts1.substvars
rm -f debian/libhts1.*.debhelper
rm -rf debian/libhts1/
rm -f debian/libhts-dev.substvars
rm -f debian/libhts-dev.*.debhelper
rm -rf debian/libhts-dev/
rm -f debian/htslib-test.substvars
rm -f debian/htslib-test.*.debhelper
rm -rf debian/htslib-test/
rm -f debian/tabix.substvars
rm -f debian/tabix.*.debhelper
rm -rf debian/tabix/
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm /<<PKGBUILDDIR>>/test/sam /<<PKGBUILDDIR>>/test/test-regidx
dh_auto_install -- \
prefix=/usr \
libdir=/usr/lib/x86_64-linux-gnu \
PACKAGE_VERSION="1.3.1-1~bpo8+1"
install -d debian/libhts1
install -d debian/libhts-dev
install -d debian/htslib-test
install -d debian/tabix
make -j2 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr libdir=/usr/lib/x86_64-linux-gnu PACKAGE_VERSION=1.3.1-1\~bpo8\+1
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/x86_64-linux-gnu /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man5 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig
if test -n ""; then mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp; fi
install -p -m 644 libhts.so /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1~bpo8+1
sed -e 's#@includedir@#/usr/include#g;s#@libdir@#/usr/lib/x86_64-linux-gnu#g;s#@PACKAGE_VERSION@#1.3.1-1~bpo8+1#g' htslib.pc.in > /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc
chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc
ln -sf libhts.so.1.3.1-1~bpo8+1 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so
ln -sf libhts.so.1.3.1-1~bpo8+1 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1
install -p bgzip htsfile tabix /<<PKGBUILDDIR>>/debian/tmp/usr/bin
if test -n ""; then install -p /<<PKGBUILDDIR>>/debian/tmp; fi
install -p -m 644 htslib/*.h /<<PKGBUILDDIR>>/debian/tmp/usr/include/htslib
install -p -m 644 libhts.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a
install -p -m 644 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
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -O--parallel
install -d debian/libhts1/usr/lib/x86_64-linux-gnu
cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1 debian/libhts1/usr/lib/x86_64-linux-gnu/
cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1\~bpo8\+1 debian/libhts1/usr/lib/x86_64-linux-gnu/
install -d debian/libhts-dev/usr/include
cp -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/
install -d debian/libhts-dev/usr/lib/x86_64-linux-gnu
cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.a debian/libhts-dev/usr/lib/x86_64-linux-gnu/
cp -a debian/tmp/usr/lib/x86_64-linux-gnu/libhts.so debian/libhts-dev/usr/lib/x86_64-linux-gnu/
install -d debian/libhts-dev/usr/share/man/man5
cp -a debian/tmp/usr/share/man/man5/faidx.5 debian/libhts-dev/usr/share/man/man5/
cp -a debian/tmp/usr/share/man/man5/sam.5 debian/libhts-dev/usr/share/man/man5/
cp -a debian/tmp/usr/share/man/man5/vcf.5 debian/libhts-dev/usr/share/man/man5/
install -d debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig
cp -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/x86_64-linux-gnu/pkgconfig/
install -d debian/htslib-test//usr/share/htslib-test
cp -a ./test/aux\#aux_java.cram debian/htslib-test//usr/share/htslib-test/
cp -a ./test/auxf\#values.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/auxf.fa debian/htslib-test//usr/share/htslib-test/
cp -a ./test/auxf.fa.fai debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1\#bounds.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1\#clip.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1\#noseq.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1\#pad1.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1\#pad2.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1\#pad3.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1\#unknown.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1.fa debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c1.fa.fai debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c2\#pad.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c2.fa debian/htslib-test//usr/share/htslib-test/
cp -a ./test/c2.fa.fai debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#1.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#2.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#5.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#5b.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#5b_java.cram debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#large_seq.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#supp.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#tag_depadded.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#tag_padded.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#unmap.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#unmap1.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce\#unmap2.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce.fa debian/htslib-test//usr/share/htslib-test/
cp -a ./test/ce.fa.fai debian/htslib-test//usr/share/htslib-test/
cp -a ./test/compare_sam.pl debian/htslib-test//usr/share/htslib-test/
cp -a ./test/cross_validate.sh debian/htslib-test//usr/share/htslib-test/
cp -a ./test/faidx.fa debian/htslib-test//usr/share/htslib-test/
cp -a ./test/fieldarith.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/fieldarith.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/formatcols.vcf debian/htslib-test//usr/share/htslib-test/
cp -a ./test/hfile.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/noroundtrip-out.vcf debian/htslib-test//usr/share/htslib-test/
cp -a ./test/noroundtrip.vcf debian/htslib-test//usr/share/htslib-test/
cp -a ./test/sam.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-regidx.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-api.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-api.out debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-hdr-in.vcf debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-hdr.out debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-sweep.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test-vcf-sweep.out debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test.pl debian/htslib-test//usr/share/htslib-test/
cp -a ./test/test_view.c debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#blank.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#large_aux.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#large_aux2.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#large_aux_java.cram debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#minimal.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#pair.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#repeated.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#rg.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#tlen.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#tlen2.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#triplet.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx\#unsorted.sam debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx.fa debian/htslib-test//usr/share/htslib-test/
cp -a ./test/xx.fa.fai debian/htslib-test//usr/share/htslib-test/
install -d debian/tabix/usr/bin
cp -a ./tabix debian/tabix/usr/bin/
cp -a ./bgzip debian/tabix/usr/bin/
dh_installdocs -O--parallel
install -g 0 -o 0 -d debian/libhts1/usr/share/doc/libhts1
install -g 0 -o 0 -m 644 -p debian/copyright debian/libhts1/usr/share/doc/libhts1/copyright
install -g 0 -o 0 -d debian/libhts-dev/usr/share/doc/libhts-dev
install -g 0 -o 0 -m 644 -p debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright
install -g 0 -o 0 -d debian/htslib-test/usr/share/doc/htslib-test
install -g 0 -o 0 -m 644 -p debian/copyright debian/htslib-test/usr/share/doc/htslib-test/copyright
install -g 0 -o 0 -d debian/tabix/usr/share/doc/tabix
install -g 0 -o 0 -m 644 -p debian/copyright debian/tabix/usr/share/doc/tabix/copyright
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installchangelogs NEWS
install -o 0 -g 0 -p -m644 debian/changelog debian/libhts1/usr/share/doc/libhts1/changelog.Debian
install -o 0 -g 0 -p -m644 NEWS debian/libhts1/usr/share/doc/libhts1/changelog
install -o 0 -g 0 -p -m644 debian/changelog debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian
install -o 0 -g 0 -p -m644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog
install -o 0 -g 0 -p -m644 debian/changelog debian/htslib-test/usr/share/doc/htslib-test/changelog.Debian
install -o 0 -g 0 -p -m644 NEWS debian/htslib-test/usr/share/doc/htslib-test/changelog
install -o 0 -g 0 -p -m644 debian/changelog debian/tabix/usr/share/doc/tabix/changelog.Debian
install -o 0 -g 0 -p -m644 NEWS debian/tabix/usr/share/doc/tabix/changelog
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -O--parallel
man --recode UTF-8 ./sam\.5 > sam\.5\.new
chmod 644 sam.5.new
mv -f sam.5.new sam.5
man --recode UTF-8 ./vcf\.5 > vcf\.5\.new
chmod 644 vcf.5.new
mv -f vcf.5.new vcf.5
man --recode UTF-8 ./faidx\.5 > faidx\.5\.new
chmod 644 faidx.5.new
mv -f faidx.5.new faidx.5
install -d debian/tabix/usr/share/man/man1/
install -p -m644 tabix.1 debian/tabix/usr/share/man/man1/tabix.1
man --recode UTF-8 ./tabix\.1 > tabix\.1\.new
chmod 644 tabix.1.new
mv -f tabix.1.new tabix.1
dh_lintian -O--parallel
install -d debian/libhts1/usr/share/lintian/overrides
install -p -m644 debian/libhts1.lintian-overrides debian/libhts1/usr/share/lintian/overrides/libhts1
install -d debian/tabix/usr/share/lintian/overrides
install -p -m644 debian/tabix.lintian-overrides debian/tabix/usr/share/lintian/overrides/tabix
dh_perl -O--parallel
(grep -s -v perl:Depends debian/htslib-test.substvars; echo perl:Depends=perl) > debian/htslib-test.substvars.new
mv debian/htslib-test.substvars.new debian/htslib-test.substvars
dh_link -O--parallel
rm -f debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1
ln -sf libhts.so.1.3.1-1\~bpo8\+1 debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1
rm -f debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so
ln -sf libhts.so.1.3.1-1\~bpo8\+1 debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.so
rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz
ln -sf tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz
dh_compress -O--parallel
cd debian/libhts1
chmod a-x usr/share/doc/libhts1/changelog.Debian usr/share/doc/libhts1/changelog
gzip -9nf usr/share/doc/libhts1/changelog.Debian usr/share/doc/libhts1/changelog
cd '/<<PKGBUILDDIR>>'
cd debian/libhts-dev
chmod a-x usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man5/faidx.5 usr/share/doc/libhts-dev/changelog.Debian usr/share/doc/libhts-dev/changelog
gzip -9nf usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man5/faidx.5 usr/share/doc/libhts-dev/changelog.Debian usr/share/doc/libhts-dev/changelog
cd '/<<PKGBUILDDIR>>'
cd debian/htslib-test
chmod a-x usr/share/doc/htslib-test/changelog.Debian usr/share/doc/htslib-test/changelog
gzip -9nf usr/share/doc/htslib-test/changelog.Debian usr/share/doc/htslib-test/changelog
cd '/<<PKGBUILDDIR>>'
cd debian/tabix
chmod a-x usr/share/man/man1/tabix.1 usr/share/doc/tabix/changelog.Debian usr/share/doc/tabix/changelog
gzip -9nf usr/share/man/man1/tabix.1 usr/share/doc/tabix/changelog.Debian usr/share/doc/tabix/changelog
cd '/<<PKGBUILDDIR>>'
dh_fixperms -O--parallel
find debian/libhts1 -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libhts1 ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts1/usr/share/doc -type f ! -regex 'debian/libhts1/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts1/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
find debian/libhts1/usr/share/man debian/libhts1/usr/man/ debian/libhts1/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts1 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts1/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts1/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts1 -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts1/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/libhts1/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/libhts1/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/libhts1/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/libhts-dev ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/libhts-dev/usr/share/doc -type f ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
find debian/libhts-dev/usr/share/man debian/libhts-dev/usr/man/ debian/libhts-dev/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/libhts-dev/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/libhts-dev/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/libhts-dev/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/htslib-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/htslib-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/htslib-test/usr/share/doc -type f ! -regex 'debian/htslib-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
find debian/htslib-test/usr/share/man debian/htslib-test/usr/man/ debian/htslib-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/htslib-test/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/htslib-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/htslib-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/tabix -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/tabix ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/tabix/usr/share/doc -type f ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
find debian/tabix/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
find debian/tabix/usr/share/man debian/tabix/usr/man/ debian/tabix/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/tabix -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/tabix/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/tabix/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
find debian/tabix -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
find debian/tabix/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/tabix/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/tabix/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
find debian/tabix/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/tabix/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 644
dh_strip -O--parallel
strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1\~bpo8\+1
strip --strip-debug debian/libhts-dev/usr/lib/x86_64-linux-gnu/libhts.a
strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/bgzip
strip --remove-section=.comment --remove-section=.note debian/tabix/usr/bin/tabix
dh_makeshlibs -O--parallel
rm -f debian/libhts1/DEBIAN/shlibs
install -d debian/libhts1/DEBIAN
echo 'libhts 1 libhts1' >>debian/libhts1/DEBIAN/shlibs
echo "# Automatically added by dh_makeshlibs">> debian/libhts1.postinst.debhelper
sed "" /usr/share/debhelper/autoscripts/postinst-makeshlibs >> debian/libhts1.postinst.debhelper
echo '# End automatically added section' >> debian/libhts1.postinst.debhelper
echo "# Automatically added by dh_makeshlibs">> debian/libhts1.postrm.debhelper
sed "" /usr/share/debhelper/autoscripts/postrm-makeshlibs >> debian/libhts1.postrm.debhelper
echo '# End automatically added section' >> debian/libhts1.postrm.debhelper
chmod 644 debian/libhts1/DEBIAN/shlibs
chown 0:0 debian/libhts1/DEBIAN/shlibs
dpkg-gensymbols -plibhts1 -Idebian/libhts1.symbols -Pdebian/libhts1 "-edebian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1~bpo8+1\
"
(grep -s -v misc:Pre-Depends debian/libhts1.substvars; echo misc:Pre-Depends=multiarch-support) > debian/libhts1.substvars.new
mv debian/libhts1.substvars.new debian/libhts1.substvars
rm -f debian/libhts-dev/DEBIAN/shlibs
rm -f debian/htslib-test/DEBIAN/shlibs
rm -f debian/tabix/DEBIAN/shlibs
dh_shlibdeps -O--parallel
dpkg-shlibdeps -Tdebian/libhts1.substvars debian/libhts1/usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1\~bpo8\+1
install -o 0 -g 0 -d debian/libhts-dev/DEBIAN
install -o 0 -g 0 -d debian/htslib-test/DEBIAN
install -o 0 -g 0 -d debian/tabix/DEBIAN
dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/tabix
dh_installdeb -O--parallel
printf '#!/bin/sh
set -e
' > debian/libhts1/DEBIAN/postinst
cat debian/libhts1.postinst.debhelper >> debian/libhts1/DEBIAN/postinst
chown 0:0 debian/libhts1/DEBIAN/postinst
chmod 755 debian/libhts1/DEBIAN/postinst
printf '#!/bin/sh
set -e
' > debian/libhts1/DEBIAN/postrm
cat debian/libhts1.postrm.debhelper >> debian/libhts1/DEBIAN/postrm
chown 0:0 debian/libhts1/DEBIAN/postrm
chmod 755 debian/libhts1/DEBIAN/postrm
dh_gencontrol -O--parallel
echo misc:Depends= >> debian/libhts1.substvars
dpkg-gencontrol -plibhts1 -ldebian/changelog -Tdebian/libhts1.substvars -Pdebian/libhts1
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 644 debian/libhts1/DEBIAN/control
chown 0:0 debian/libhts1/DEBIAN/control
echo misc:Depends= >> debian/libhts-dev.substvars
dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 644 debian/libhts-dev/DEBIAN/control
chown 0:0 debian/libhts-dev/DEBIAN/control
echo misc:Depends= >> debian/htslib-test.substvars
dpkg-gencontrol -phtslib-test -ldebian/changelog -Tdebian/htslib-test.substvars -Pdebian/htslib-test
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 644 debian/htslib-test/DEBIAN/control
chown 0:0 debian/htslib-test/DEBIAN/control
echo misc:Depends= >> debian/tabix.substvars
dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
chmod 644 debian/tabix/DEBIAN/control
chown 0:0 debian/tabix/DEBIAN/control
dh_md5sums -O--parallel
(cd debian/libhts1 >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 644 debian/libhts1/DEBIAN/md5sums
chown 0:0 debian/libhts1/DEBIAN/md5sums
(cd debian/libhts-dev >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 644 debian/libhts-dev/DEBIAN/md5sums
chown 0:0 debian/libhts-dev/DEBIAN/md5sums
(cd debian/htslib-test >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 644 debian/htslib-test/DEBIAN/md5sums
chown 0:0 debian/htslib-test/DEBIAN/md5sums
(cd debian/tabix >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 644 debian/tabix/DEBIAN/md5sums
chown 0:0 debian/tabix/DEBIAN/md5sums
dh_builddeb -O--parallel
dpkg-deb --build debian/libhts1 ..
dpkg-deb --build debian/libhts-dev ..
dpkg-deb: building package `libhts-dev' in `../libhts-dev_1.3.1-1~bpo8+1_amd64.deb'.
dpkg-deb: building package `libhts1' in `../libhts1_1.3.1-1~bpo8+1_amd64.deb'.
dpkg-deb --build debian/htslib-test ..
dpkg-deb: building package `htslib-test' in `../htslib-test_1.3.1-1~bpo8+1_all.deb'.
dpkg-deb --build debian/tabix ..
dpkg-deb: building package `tabix' in `../tabix_1.3.1-1~bpo8+1_amd64.deb'.
dpkg-genchanges -v1.3-1~bpo8+1 >../htslib_1.3.1-1~bpo8+1_amd64.changes
dpkg-genchanges: not including original source code in upload
dpkg-source --after-build htslib-1.3.1
dpkg-source: info: using options from htslib-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md)$
dpkg-buildpackage: binary and diff upload (original source NOT included)
--------------------------------------------------------------------------------
Build finished at 20160508-1403
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
htslib_1.3.1-1~bpo8+1_amd64.changes:
------------------------------------
Format: 1.8
Date: Sun, 08 May 2016 21:28:33 +0900
Source: htslib
Binary: libhts1 libhts-dev htslib-test tabix
Architecture: source amd64 all
Version: 1.3.1-1~bpo8+1
Distribution: jessie-backports
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
htslib-test - Test data for HTSlib
libhts-dev - Development files for the HTSlib
libhts1 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Changes:
htslib (1.3.1-1~bpo8+1) jessie-backports; urgency=medium
.
* Rebuild for jessie-backports.
.
htslib (1.3.1-1) unstable; urgency=medium
.
36bf59a Merge tag '1.3.1' into debian/unstable
559f8b4 Remove add_largefile.patch, applied upstream.
7163afb Update symbols file. Missing _vcf_parse_format at Base and fai_read at Base.
c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev.
3b219b8 Enable libcurl.
9101580 Conforms to the Policy version 3.9.8.
.
htslib (1.3-2) unstable; urgency=medium
.
* Team upload
.
[ Steffen Moeller and Jon Ison ]
* Introduction of EDAM annotation
.
[ Sascha Steinbiss ]
* Include upstream patch for large file support
* Run configure as part of the build
Checksums-Sha1:
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310d59963cc32a3e1a7f7d0ed605d9b72b86ee10 258274 libhts1_1.3.1-1~bpo8+1_amd64.deb
239456eae30f7ebd0b51baa4064a5a060c16f136 314518 libhts-dev_1.3.1-1~bpo8+1_amd64.deb
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f6a9ef47c4c40ae11c3c4b71953c8e9a03d4b696 252512 tabix_1.3.1-1~bpo8+1_amd64.deb
Checksums-Sha256:
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0d9042864ed450aced897c28619b41be0f59a01bcd2e54fc81de469c768c97ea 10184 htslib_1.3.1-1~bpo8+1.debian.tar.xz
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Files:
20fdd8e86fb45c40c948d18be2ab2705 1297 science optional htslib_1.3.1-1~bpo8+1.dsc
4e640df2495ac0db5f05185adf0503de 10184 science optional htslib_1.3.1-1~bpo8+1.debian.tar.xz
e775e6f537ddc42dd5a98c44e6cbb34d 258274 libs optional libhts1_1.3.1-1~bpo8+1_amd64.deb
f0328cdee36237653c3c6ffebdd6f49d 314518 libdevel optional libhts-dev_1.3.1-1~bpo8+1_amd64.deb
235bb571c18167415039e985724bc871 541970 science optional htslib-test_1.3.1-1~bpo8+1_all.deb
5d8de035b31a8e2ab6e915508f8bf1c9 252512 science optional tabix_1.3.1-1~bpo8+1_amd64.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libhts1_1.3.1-1~bpo8+1_amd64.deb
--------------------------------
new debian package, version 2.0.
size 258274 bytes: control archive=5305 bytes.
1041 bytes, 22 lines control
365 bytes, 5 lines md5sums
135 bytes, 7 lines * postinst #!/bin/sh
132 bytes, 7 lines * postrm #!/bin/sh
17 bytes, 1 lines shlibs
16657 bytes, 637 lines symbols
Package: libhts1
Source: htslib
Version: 1.3.1-1~bpo8+1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 685
Pre-Depends: multiarch-support
Depends: libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), libssl1.0.0 (>= 1.0.0), zlib1g (>= 1:1.2.0.2)
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 2016-05-08 14:03 ./
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/
lrwxrwxrwx root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.so.1 -> libhts.so.1.3.1-1~bpo8+1
-rw-r--r-- root/root 633152 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.so.1.3.1-1~bpo8+1
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/libhts1/
-rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/libhts1/changelog.Debian.gz
-rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/libhts1/changelog.gz
-rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/libhts1/copyright
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 105 2016-05-08 13:48 ./usr/share/lintian/overrides/libhts1
libhts-dev_1.3.1-1~bpo8+1_amd64.deb
-----------------------------------
new debian package, version 2.0.
size 314518 bytes: control archive=1758 bytes.
1037 bytes, 24 lines control
1924 bytes, 30 lines md5sums
Package: libhts-dev
Source: htslib
Version: 1.3.1-1~bpo8+1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1176
Depends: libhts1 (= 1.3.1-1~bpo8+1)
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.
drwxr-xr-x root/root 0 2016-05-08 14:03 ./
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/include/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/include/htslib/
-rw-r--r-- root/root 11423 2016-04-22 01:45 ./usr/include/htslib/bgzf.h
-rw-r--r-- root/root 14648 2016-04-22 01:45 ./usr/include/htslib/cram.h
-rw-r--r-- root/root 4562 2016-04-22 01:45 ./usr/include/htslib/faidx.h
-rw-r--r-- root/root 7111 2016-04-22 01:45 ./usr/include/htslib/hfile.h
-rw-r--r-- root/root 21950 2016-04-22 01:45 ./usr/include/htslib/hts.h
-rw-r--r-- root/root 2451 2016-04-22 01:45 ./usr/include/htslib/hts_defs.h
-rw-r--r-- root/root 4195 2016-04-22 01:45 ./usr/include/htslib/kbitset.h
-rw-r--r-- root/root 2716 2016-04-22 01:45 ./usr/include/htslib/kfunc.h
-rw-r--r-- root/root 21540 2016-04-22 01:45 ./usr/include/htslib/khash.h
-rw-r--r-- root/root 3990 2016-04-22 01:45 ./usr/include/htslib/khash_str2int.h
-rw-r--r-- root/root 5086 2016-04-22 01:45 ./usr/include/htslib/klist.h
-rw-r--r-- root/root 2828 2016-04-22 01:45 ./usr/include/htslib/knetfile.h
-rw-r--r-- root/root 8900 2016-04-22 01:45 ./usr/include/htslib/kseq.h
-rw-r--r-- root/root 10125 2016-04-22 01:45 ./usr/include/htslib/ksort.h
-rw-r--r-- root/root 7071 2016-04-22 01:45 ./usr/include/htslib/kstring.h
-rw-r--r-- root/root 5798 2016-04-22 01:45 ./usr/include/htslib/regidx.h
-rw-r--r-- root/root 17089 2016-04-22 01:45 ./usr/include/htslib/sam.h
-rw-r--r-- root/root 12666 2016-04-22 01:45 ./usr/include/htslib/synced_bcf_reader.h
-rw-r--r-- root/root 2910 2016-04-22 01:45 ./usr/include/htslib/tbx.h
-rw-r--r-- root/root 39884 2016-04-22 01:45 ./usr/include/htslib/vcf.h
-rw-r--r-- root/root 1586 2016-04-22 01:45 ./usr/include/htslib/vcf_sweep.h
-rw-r--r-- root/root 4659 2016-04-22 01:45 ./usr/include/htslib/vcfutils.h
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/
-rw-r--r-- root/root 921556 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.a
lrwxrwxrwx root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/libhts.so -> libhts.so.1.3.1-1~bpo8+1
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/pkgconfig/
-rw-r--r-- root/root 279 2016-05-08 14:03 ./usr/lib/x86_64-linux-gnu/pkgconfig/htslib.pc
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/libhts-dev/
-rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/libhts-dev/changelog.Debian.gz
-rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/libhts-dev/changelog.gz
-rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/libhts-dev/copyright
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/man5/
-rw-r--r-- root/root 2080 2016-05-08 14:03 ./usr/share/man/man5/faidx.5.gz
-rw-r--r-- root/root 1535 2016-05-08 14:03 ./usr/share/man/man5/sam.5.gz
-rw-r--r-- root/root 1854 2016-05-08 14:03 ./usr/share/man/man5/vcf.5.gz
htslib-test_1.3.1-1~bpo8+1_all.deb
----------------------------------
new debian package, version 2.0.
size 541970 bytes: control archive=2709 bytes.
944 bytes, 22 lines control
4585 bytes, 66 lines md5sums
Package: htslib-test
Source: htslib
Version: 1.3.1-1~bpo8+1
Architecture: all
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 4180
Depends: perl
Section: science
Priority: optional
Homepage: https://github.com/samtools/htslib
Description: Test data for HTSlib
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
Format), used for high-throughput sequencing data, and is the core library
used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
compatible with gcc, g++ and clang.
.
HTSlib implements a generalized BAM (binary SAM) index, with file extension
‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
new index and then for the old if the new index is absent.
.
This package contains test files and scripts for the HTSlib.
drwxr-xr-x root/root 0 2016-05-08 14:03 ./
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/htslib-test/
-rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/htslib-test/changelog.Debian.gz
-rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/htslib-test/changelog.gz
-rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/htslib-test/copyright
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-rw-r--r-- root/root 3774 2016-04-22 01:45 ./usr/share/htslib-test/aux#aux_java.cram
-rw-r--r-- root/root 727 2016-04-22 01:45 ./usr/share/htslib-test/auxf#values.sam
-rw-r--r-- root/root 29 2016-04-22 01:45 ./usr/share/htslib-test/auxf.fa
-rw-r--r-- root/root 18 2016-04-22 01:45 ./usr/share/htslib-test/auxf.fa.fai
-rw-r--r-- root/root 148 2016-04-22 01:45 ./usr/share/htslib-test/c1#bounds.sam
-rw-r--r-- root/root 337 2016-04-22 01:45 ./usr/share/htslib-test/c1#clip.sam
-rw-r--r-- root/root 433 2016-04-22 01:45 ./usr/share/htslib-test/c1#noseq.sam
-rw-r--r-- root/root 388 2016-04-22 01:45 ./usr/share/htslib-test/c1#pad1.sam
-rw-r--r-- root/root 527 2016-04-22 01:45 ./usr/share/htslib-test/c1#pad2.sam
-rw-r--r-- root/root 665 2016-04-22 01:45 ./usr/share/htslib-test/c1#pad3.sam
-rw-r--r-- root/root 429 2016-04-22 01:45 ./usr/share/htslib-test/c1#unknown.sam
-rw-r--r-- root/root 15 2016-04-22 01:45 ./usr/share/htslib-test/c1.fa
-rw-r--r-- root/root 14 2016-04-22 01:45 ./usr/share/htslib-test/c1.fa.fai
-rw-r--r-- root/root 847 2016-04-22 01:45 ./usr/share/htslib-test/c2#pad.sam
-rw-r--r-- root/root 14 2016-04-22 01:45 ./usr/share/htslib-test/c2.fa
-rw-r--r-- root/root 12 2016-04-22 01:45 ./usr/share/htslib-test/c2.fa.fai
-rw-r--r-- root/root 341 2016-04-22 01:45 ./usr/share/htslib-test/ce#1.sam
-rw-r--r-- root/root 645 2016-04-22 01:45 ./usr/share/htslib-test/ce#2.sam
-rw-r--r-- root/root 1872 2016-04-22 01:45 ./usr/share/htslib-test/ce#5.sam
-rw-r--r-- root/root 1836 2016-04-22 01:45 ./usr/share/htslib-test/ce#5b.sam
-rw-r--r-- root/root 6784 2016-04-22 01:45 ./usr/share/htslib-test/ce#5b_java.cram
-rw-r--r-- root/root 2147244 2016-04-22 01:45 ./usr/share/htslib-test/ce#large_seq.sam
-rw-r--r-- root/root 547 2016-04-22 01:45 ./usr/share/htslib-test/ce#supp.sam
-rw-r--r-- root/root 1638 2016-04-22 01:45 ./usr/share/htslib-test/ce#tag_depadded.sam
-rw-r--r-- root/root 1650 2016-04-22 01:45 ./usr/share/htslib-test/ce#tag_padded.sam
-rw-r--r-- root/root 1325 2016-04-22 01:45 ./usr/share/htslib-test/ce#unmap.sam
-rw-r--r-- root/root 2747 2016-04-22 01:45 ./usr/share/htslib-test/ce#unmap1.sam
-rw-r--r-- root/root 5525 2016-04-22 01:45 ./usr/share/htslib-test/ce#unmap2.sam
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-rwxr-xr-x root/root 3204 2016-04-22 01:45 ./usr/share/htslib-test/cross_validate.sh
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-rw-r--r-- root/root 240 2016-04-22 01:45 ./usr/share/htslib-test/formatcols.vcf
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-rw-r--r-- root/root 325 2016-04-22 01:45 ./usr/share/htslib-test/noroundtrip-out.vcf
-rw-r--r-- root/root 271 2016-04-22 01:45 ./usr/share/htslib-test/noroundtrip.vcf
-rw-r--r-- root/root 7440 2016-04-22 01:45 ./usr/share/htslib-test/sam.c
-rw-r--r-- root/root 4292 2016-04-22 01:45 ./usr/share/htslib-test/test-regidx.c
-rw-r--r-- root/root 10142 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-api.c
-rw-r--r-- root/root 1936 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-api.out
-rw-r--r-- root/root 2024 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-hdr-in.vcf
-rw-r--r-- root/root 1349 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-hdr.out
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-rw-r--r-- root/root 92 2016-04-22 01:45 ./usr/share/htslib-test/test-vcf-sweep.out
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-rw-r--r-- root/root 6405 2016-04-22 01:45 ./usr/share/htslib-test/test_view.c
-rw-r--r-- root/root 0 2016-04-22 01:45 ./usr/share/htslib-test/xx#blank.sam
-rw-r--r-- root/root 905485 2016-04-22 01:45 ./usr/share/htslib-test/xx#large_aux.sam
-rw-r--r-- root/root 651 2016-04-22 01:45 ./usr/share/htslib-test/xx#large_aux2.sam
-rw-r--r-- root/root 22668 2016-04-22 01:45 ./usr/share/htslib-test/xx#large_aux_java.cram
-rw-r--r-- root/root 254 2016-04-22 01:45 ./usr/share/htslib-test/xx#minimal.sam
-rw-r--r-- root/root 304 2016-04-22 01:45 ./usr/share/htslib-test/xx#pair.sam
-rw-r--r-- root/root 298 2016-04-22 01:45 ./usr/share/htslib-test/xx#repeated.sam
-rw-r--r-- root/root 517 2016-04-22 01:45 ./usr/share/htslib-test/xx#rg.sam
-rw-r--r-- root/root 1028 2016-04-22 01:45 ./usr/share/htslib-test/xx#tlen.sam
-rw-r--r-- root/root 1096 2016-04-22 01:45 ./usr/share/htslib-test/xx#tlen2.sam
-rw-r--r-- root/root 267 2016-04-22 01:45 ./usr/share/htslib-test/xx#triplet.sam
-rw-r--r-- root/root 320 2016-04-22 01:45 ./usr/share/htslib-test/xx#unsorted.sam
-rw-r--r-- root/root 51 2016-04-22 01:45 ./usr/share/htslib-test/xx.fa
-rw-r--r-- root/root 29 2016-04-22 01:45 ./usr/share/htslib-test/xx.fa.fai
tabix_1.3.1-1~bpo8+1_amd64.deb
------------------------------
new debian package, version 2.0.
size 252512 bytes: control archive=1028 bytes.
908 bytes, 19 lines control
433 bytes, 7 lines md5sums
Package: tabix
Source: htslib
Version: 1.3.1-1~bpo8+1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1016
Depends: libc6 (>= 2.15), libcurl3-gnutls (>= 7.18.0), libssl1.0.0 (>= 1.0.0), zlib1g (>= 1:1.2.0.2)
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 version of tabix is built from the HTSlib source.
drwxr-xr-x root/root 0 2016-05-08 14:03 ./
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/bin/
-rwxr-xr-x root/root 445712 2016-05-08 14:03 ./usr/bin/bgzip
-rwxr-xr-x root/root 536008 2016-05-08 14:03 ./usr/bin/tabix
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/doc/tabix/
-rw-r--r-- root/root 1561 2016-05-08 13:48 ./usr/share/doc/tabix/changelog.Debian.gz
-rw-r--r-- root/root 2350 2016-04-22 01:45 ./usr/share/doc/tabix/changelog.gz
-rw-r--r-- root/root 5776 2016-05-08 13:48 ./usr/share/doc/tabix/copyright
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 129 2015-09-07 16:20 ./usr/share/lintian/overrides/tabix
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/
drwxr-xr-x root/root 0 2016-05-08 14:03 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2016-05-08 14:03 ./usr/share/man/man1/bgzip.1.gz -> tabix.1.gz
-rw-r--r-- root/root 2797 2016-05-08 14:03 ./usr/share/man/man1/tabix.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: amd64
Build-Space: 50084
Build-Time: 314
Distribution: jessie-backports
Host Architecture: amd64
Install-Time: 198
Job: /home/afif/مشاريع/debian/med/htslib/htslib_1.3.1-1~bpo8+1.dsc
Machine Architecture: amd64
Package: htslib
Package-Time: 539
Source-Version: 1.3.1-1~bpo8+1
Space: 50084
Status: successful
Version: 1.3.1-1~bpo8+1
--------------------------------------------------------------------------------
Finished at 20160508-1403
Build needed 00:08:59, 50084k disc space
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