[med-svn] [htslib] 02/11: New upstream version 1.5
Andreas Tille
tille at debian.org
Mon Dec 11 13:58:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository htslib.
commit a7cd55f9ac9547247c576431fe1d235615a5ddc3
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 11 14:15:59 2017 +0100
New upstream version 1.5
---
debian/README.source | 37 --
debian/changelog | 268 -----------
debian/compat | 1 -
debian/control | 109 -----
debian/copyright | 116 -----
debian/gbp.conf | 15 -
debian/htslib-test.install | 6 -
debian/libhts-dev.install | 6 -
debian/libhts-dev.links | 5 -
debian/libhts-private-dev.install | 1 -
debian/libhts2.install | 2 -
debian/libhts2.lintian-overrides | 2 -
debian/libhts2.symbols | 710 ----------------------------
debian/patches/877670.patch | 34 --
debian/patches/define_PATH_MAX.patch | 37 --
debian/patches/fPIC.patch | 16 -
debian/patches/fix_pkg-config.patch | 21 -
debian/patches/htslib-add-cram_to_bam.patch | 28 --
debian/patches/literal_version.patch | 16 -
debian/patches/series | 5 -
debian/rules | 52 --
debian/source/format | 1 -
debian/source/options | 2 -
debian/tabix.install | 3 -
debian/tabix.links | 1 -
debian/tabix.lintian-overrides | 3 -
debian/tabix.manpages | 2 -
debian/tests/control | 3 -
debian/tests/run-unit-test | 19 -
debian/upstream/metadata | 15 -
debian/upstream/tabix.edam | 16 -
debian/watch | 3 -
32 files changed, 1555 deletions(-)
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 4d5e090..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,37 +0,0 @@
-Since this Git repository does not follow the usual Debian Med
-workflow it is documented here, how the package can be updated:
-
- 1. in the master branch, pull the upstream master branch and its tags.
-
- git checkout master
- git pull https://github.com/samtools/htslib --tags
-
- Remark: If this pull fails with a lot of stuff to merge you might
- have some ~/.gitconfig that breaks the pull above. Please try to
- deactivate it for the moment.
-
- 2. Merge the tag in the debian/unstable branch
-
- git checkout debian/unstable ; git merge <version>
-
- 3. download the upstream tarball
-
- uscan --force-download
-
- 4. Register the upstream tarball in the pristine-tar branch directly with
- the pristine-tar command directly (stay in master branch when doing this)
-
- pristine-tar commit ../htslib_<version>.orig.tar.gz <version>
-
- Remark by Andreas Tille: To make this work you need to create a branch
- upstream at least in your local clone.
-
- 5. Update the packaging files, build with gbp - debian-branch and
- upstream-branch are properly set in debian/gbp.conf
-
-According to Charles Plessy this workflow has the advantage to propose
-upstream via pull requests on GitHub. The Debian Med policy currently
-does only contain a short paragraph to mention the derived workflow:
-
- http://debian-med.alioth.debian.org/docs/policy.html#git-without-tarball
-
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 7510331..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,268 +0,0 @@
-htslib (1.5-6) unstable; urgency=medium
-
- * Do not install htslib*.mk fragments
- Closes: #881360
-
- -- Andreas Tille <tille at debian.org> Mon, 11 Dec 2017 13:58:23 +0100
-
-htslib (1.5-5) unstable; urgency=medium
-
- [ Graham Inggs ]
- * Extend i386 fix to hurd and kfreebsd
-
- [ Helmut Grohne ]
- * Fix FTCBFS: Let dh_auto_configure pass --host to ./configure
- Closes: #879885
-
- [ Andreas Tille ]
- * Fix issues with private cram headers
- - Provide cram headers in separate package libhts-private-dev.install
- Closes: #881170
- - Deactivate fix_pkg-config.patch
- Closes: #881359
- * Standards-Version: 4.1.2
-
- -- Andreas Tille <tille at debian.org> Sun, 10 Dec 2017 09:00:27 +0100
-
-htslib (1.5-4) unstable; urgency=medium
-
- * Fix build on i386 (Thanks to Graham Inggs <ginggs at debian.org>)
- Closes: #881149
-
- -- Andreas Tille <tille at debian.org> Mon, 20 Nov 2017 22:42:09 +0100
-
-htslib (1.5-3) unstable; urgency=medium
-
- * Team upload
-
- [ Diane Trout ]
- * Restore libhts2.symbols and update for changes from 1.4.1 and 1.5
- versions of htslib. (Closes: #879886)
-
- [ Graham Inggs ]
- * Update 877670.patch as it was applied upstream
-
- -- Diane Trout <diane at ghic.org> Fri, 10 Nov 2017 12:38:12 +0100
-
-htslib (1.5-2) unstable; urgency=medium
-
- * Apply patch provided by Graham Inggs <ginggs at debian.org> to fix FTBFS
- on armel armhf and ppc64el of bcftools
- Closes: #877670
- * Standards-Version: 4.1.1
- -- Andreas Tille <tille at debian.org> Wed, 08 Nov 2017 08:24:26 +0100
-
-htslib (1.5-1) unstable; urgency=medium
-
- * Team upload
-
- [ Andreas Tille ]
- * New upstream version
- * Standards-Version: 4.0.0 (no changes needed)
- * do not parse d/changelog explicitly
- * hardening=+all
- * install htslib*.mk files that are used in bcftools
-
- [ Steffen Moeller ]
- * [upstream/metadata] Added reference to OMICtools
-
- [ Matthias Klumpp ]
- * libhts-dev: Depend on missing liblzma-dev
- * Wrap and sort
-
- -- Matthias Klumpp <mak at debian.org> Thu, 03 Aug 2017 22:56:42 -0400
-
-htslib (1.4.1-5) unstable; urgency=medium
-
- * Team upload
- * Dereference symlinks to fix autopkgtest (Closes: #866137)
-
- -- Graham Inggs <ginggs at debian.org> Wed, 19 Jul 2017 10:37:52 +0200
-
-htslib (1.4.1-4) unstable; urgency=medium
-
- * Team upload
- * Fix FTBFS on s390x and sparc64, thanks Adrian Bunk (Closes: #865010)
-
- -- Graham Inggs <ginggs at debian.org> Tue, 18 Jul 2017 00:49:30 +0200
-
-htslib (1.4.1-3) unstable; urgency=medium
-
- * Team upload.
- * Fix FTBFS on i386. Thanks to Adrian Bunk for the patch.
- Closes: #865012
-
- -- Sascha Steinbiss <satta at debian.org> Mon, 17 Jul 2017 18:25:56 +0200
-
-htslib (1.4.1-2) unstable; urgency=medium
-
- * Create symlinks only for arch=indep target when target dir exists
- Closes: #864979
-
- -- Andreas Tille <tille at debian.org> Sun, 18 Jun 2017 14:19:22 +0200
-
-htslib (1.4.1-1) unstable; urgency=medium
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Sun, 18 Jun 2017 00:17:35 +0200
-
-htslib (1.4-3) experimental; urgency=medium
-
- * add the cram_to_bam function to the public interface of htslib because
- it is used by code in Sambamba
-
- -- Andreas Tille <tille at debian.org> Thu, 04 May 2017 10:57:31 +0200
-
-htslib (1.4-2) experimental; urgency=medium
-
- * Include htsfile binary into tabix package since its used by manta
- package
-
- -- Andreas Tille <tille at debian.org> Tue, 02 May 2017 15:42:11 +0200
-
-htslib (1.4-1) experimental; urgency=medium
-
- * New upstream version
- * Drop autoconf from Build-Depends
- * Add libbz2-dev and liblzma-dev to Build-Depends
- * Remove binary files from test results
- * Remove symbols file
- * Change library name to match soname
-
- -- Andreas Tille <tille at debian.org> Tue, 21 Mar 2017 17:44:03 +0100
-
-htslib (1.3.2-3) experimental; urgency=medium
-
- * Install header files from cram dir in -dev package since these are
- used in libseqlib
- * Fix pkg-config
-
- -- Andreas Tille <tille at debian.org> Fri, 10 Feb 2017 08:46:29 +0100
-
-htslib (1.3.2-2) unstable; urgency=medium
-
- * Add build-essential and @builddeps@ to autopkgtest
- * debhelper 10
- * d/watch: version=4
-
- -- Andreas Tille <tille at debian.org> Sat, 14 Jan 2017 19:23:52 +0100
-
-htslib (1.3.2-1) unstable; urgency=medium
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Fri, 04 Nov 2016 12:58:19 +0100
-
-htslib (1.3.1-3) unstable; urgency=medium
-
- * Fix build on hurd (thanks for the patch to Svante Signell
- <svante.signell at gmail.com>)
- Closes: #836190
- * Add myself to uploaders
-
- -- Andreas Tille <tille at debian.org> Thu, 01 Sep 2016 10:01:23 +0200
-
-htslib (1.3.1-2) unstable; urgency=medium
-
- [ Canberk Koç ]
- * Team upload.
- * Autopktest added
-
- [ Andreas Tille ]
- * hardening=+bindnow
-
- -- Canberk Koç <canberkkoc at gmail.com> Wed, 03 Aug 2016 04:21:17 +0300
-
-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.
-
- -- Charles Plessy <plessy at debian.org> Mon, 25 Apr 2016 22:28:11 +0900
-
-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
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Mon, 08 Feb 2016 16:46:35 +0000
-
-htslib (1.3-1) unstable; urgency=medium
-
- * Team upload
- * New upstream version
- * Ignore metadata files different between git and tarball
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 30 Jan 2016 12:16:06 +0000
-
-htslib (1.2.1-2) unstable; urgency=medium
-
- * Team upload
- * Enable build on hurd-i386
- Closes: #793512
- * More verbose description vor -dev and -test package
- * Fix lintian override
- * Verified Mayhem bug report which is solved in this version
- Closes: #716376
-
- -- Andreas Tille <tille at debian.org> Wed, 09 Dec 2015 17:00:47 +0100
-
-htslib (1.2.1-1) unstable; urgency=medium
-
- 0662716 Merge tag '1.2.1' into debian/unstable
- 084f27d Install NEWS as upstream changelog.
- 316fb96 Override a Lintian false positive.
- 3363679 Clean test directory.
- 69bf167 Corrected a typo in tabix description.
-
- -- Charles Plessy <plessy at debian.org> Mon, 25 May 2015 13:35:03 +0900
-
-htslib (1.1-1) unstable; urgency=medium
-
- 1357fbd Merge tag '1.1' into debian/unstable
- 87549cd Updated symbols file. One symbol is missing.
- 873ea9b Removed orphan paragraph in machine-readable copyright file.
- 49de2b9 Allow parallel build.
- 7fe3bb5 Normalise control file (VCS-Browser, Pre-Depends).
- 0e5e9e6 Conforms to Policy 3.9.6.
-
- -- Charles Plessy <plessy at debian.org> Wed, 24 Sep 2014 21:24:11 +0900
-
-htslib (1.0-2) unstable; urgency=medium
-
- Uploaded to unstable (see previous changelog from experimental).
-
- -- Charles Plessy <plessy at debian.org> Tue, 16 Sep 2014 20:27:04 +0900
-
-htslib (1.0-1) experimental; urgency=low
-
- cc559b8 Merged with upstream's master branch.
- 74b9d7b Build on the master branch.
- 04815a7 New major version (libhts0 -> libhts1).
- 98c18ca Updated symbols file.
- 22fef0c Install pkgconfig file.
- 420896b Override PACKAGE_VERSION to avoid tags with a slash in the name.
- 79b5d4e Use the Debian package version as PACKAGE_VERSION.
- 72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode.
- d870946 Adjusted substitution variables following dpkg's warnings.
- 9469458 Removed debug command accidentally introduced.
- 8c7f7d4 Replace the old tabix package from the tabix source package.
-
- -- Charles Plessy <plessy at debian.org> Sun, 17 Aug 2014 20:12:28 +0900
-
-htslib (0.2.0~rc3-1) unstable; urgency=low
-
- * Initial release. (Closes: #729282)
-
- -- Charles Plessy <plessy at debian.org> Sat, 16 Nov 2013 15:35:03 +0900
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index f599e28..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-10
diff --git a/debian/control b/debian/control
deleted file mode 100644
index b49f8f5..0000000
--- a/debian/control
+++ /dev/null
@@ -1,109 +0,0 @@
-Source: htslib
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 10),
- dh-exec,
- libbz2-dev,
- libcurl4-gnutls-dev,
- liblzma-dev,
- libssl-dev,
- zlib1g-dev
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/htslib.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/htslib.git -b debian/unstable
-Homepage: https://github.com/samtools/htslib
-
-Package: libhts2
-Architecture: any
-Multi-Arch: same
-Section: libs
-Depends: ${misc:Depends},
- ${shlibs:Depends}
-Pre-Depends: ${misc:Pre-Depends}
-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.
-
-Package: libhts-dev
-Architecture: any
-Multi-Arch: same
-Section: libdevel
-Depends: libhts2 (= ${binary:Version}),
- liblzma-dev,
- tabix,
- ${misc:Depends}
-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.
-
-Package: libhts-private-dev
-Architecture: all
-Section: libdevel
-Depends: libhts-dev (>= 1.5-5),
- ${misc:Depends}
-Breaks: libhts-dev (<= 1.5-4)
-Description: private development files for the HTSlib (use with care)
- 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 private header files for the HTSlib. They are *not*
- intended for general use but libseqlib needs these files.
-
-Package: htslib-test
-Architecture: all
-Depends: libhts-private-dev,
- ${misc:Depends},
- ${perl:Depends}
-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.
-
-Package: tabix
-Architecture: any
-Depends: ${misc:Depends},
- ${shlibs:Depends}
-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.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 21f0a4b..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,116 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: https://github.com/samtools/htslib/archive/1.3.1.tar.gz
-
-Files: *
-Copyright: © 2012-2016 Genome Research Ltd.
- © 2008-2013 Broad Institute / Massachusetts Institute of Technology
- © The Wellcome Trust Sanger Institute
- © 2008-2012 by Attractive Chaos <attractor at live.co.uk>
-License: MIT
-
-Files: cram/*
-Copyright: © 2012-2014 Genome Research Ltd.
- © 1995-2003 MEDICAL RESEARCH COUNCIL
-License: Various_BSD-3-Clause
- The files in the 'cram' directory are under one or both of the following
- licenses.
- .
- ---------------------------------------------------------------------------
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
- 1. Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- .
- 2. Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- .
- 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
- Institute nor the names of its contributors may be used to endorse or promote
- products derived from this software without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- .
- ---------------------------------------------------------------------------
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
- 1 Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- .
- 2 Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- .
- 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
- MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
- promote products derived from this software without specific prior written
- permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Files: md5.c
-Copyright: No copyright is claimed
-License: solar-MD5
- This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
- MD5 Message-Digest Algorithm (RFC 1321).
- .
- Homepage:
- http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
- .
- Author:
- Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
- .
- This software was written by Alexander Peslyak in 2001. No copyright is
- claimed, and the software is hereby placed in the public domain.
- In case this attempt to disclaim copyright and place the software in the
- public domain is deemed null and void, then the software is
- Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
- general public under the following terms:
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted.
- .
- There's ABSOLUTELY NO WARRANTY, express or implied.
-
-License: MIT
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
- .
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
diff --git a/debian/gbp.conf b/debian/gbp.conf
deleted file mode 100644
index 533b176..0000000
--- a/debian/gbp.conf
+++ /dev/null
@@ -1,15 +0,0 @@
-# This package uses pristine-tar, and does not follow the canonical layout of git-buildpackage.
-
-[DEFAULT]
-# the default branch for upstream sources:
-upstream-branch = master
-# the default branch for the debian patch:
-debian-branch = debian/unstable
-# the default tag formats used:
-upstream-tag = %(version)s
-# use pristine-tar:
-pristine-tar = True
-
-[dch]
-# include 7 digits of the commit id in the changelog enty:
-id-length = 7
diff --git a/debian/htslib-test.install b/debian/htslib-test.install
deleted file mode 100644
index 70a9e9b..0000000
--- a/debian/htslib-test.install
+++ /dev/null
@@ -1,6 +0,0 @@
-*.c /usr/share/htslib-test
-*.h /usr/share/htslib-test
-*.mk /usr/share/htslib-test
-Makefile /usr/share/htslib-test
-cram/*.c /usr/share/htslib-test/cram
-test/* /usr/share/htslib-test/test
diff --git a/debian/libhts-dev.install b/debian/libhts-dev.install
deleted file mode 100755
index 87e7d23..0000000
--- a/debian/libhts-dev.install
+++ /dev/null
@@ -1,6 +0,0 @@
-#! /usr/bin/dh-exec
-usr/include/* usr/include
-usr/lib/${DEB_HOST_MULTIARCH}/*.a usr/lib/${DEB_HOST_MULTIARCH}
-usr/lib/${DEB_HOST_MULTIARCH}/*.so usr/lib/${DEB_HOST_MULTIARCH}
-usr/share/man/man5/* usr/share/man/man5
-usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig/htslib.pc usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig
diff --git a/debian/libhts-dev.links b/debian/libhts-dev.links
deleted file mode 100755
index 926edb3..0000000
--- a/debian/libhts-dev.links
+++ /dev/null
@@ -1,5 +0,0 @@
-#! /usr/bin/dh-exec
-usr/lib/${DEB_HOST_MULTIARCH}/libhts.a usr/lib/htslib/libhts.a
-usr/bin/tabix usr/lib/htslib/tabix
-usr/bin/bgzip usr/lib/htslib/bgzip
-usr/include/htslib usr/lib/htslib/htslib
diff --git a/debian/libhts-private-dev.install b/debian/libhts-private-dev.install
deleted file mode 100644
index 3d2e3e2..0000000
--- a/debian/libhts-private-dev.install
+++ /dev/null
@@ -1 +0,0 @@
-cram/*.h usr/include/htslib/cram
diff --git a/debian/libhts2.install b/debian/libhts2.install
deleted file mode 100755
index 659d59c..0000000
--- a/debian/libhts2.install
+++ /dev/null
@@ -1,2 +0,0 @@
-#! /usr/bin/dh-exec
-usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH}
diff --git a/debian/libhts2.lintian-overrides b/debian/libhts2.lintian-overrides
deleted file mode 100644
index 20ec47c..0000000
--- a/debian/libhts2.lintian-overrides
+++ /dev/null
@@ -1,2 +0,0 @@
-# False positive
-libhts2: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libhts.so.* compres compress
diff --git a/debian/libhts2.symbols b/debian/libhts2.symbols
deleted file mode 100644
index 9e02ba1..0000000
--- a/debian/libhts2.symbols
+++ /dev/null
@@ -1,710 +0,0 @@
-libhts.so.2 libhts2 #MINVER#
- _reader_next_line at Base 1.0
- _regidx_build_index at Base 1.2.1
- bam_aux2A at Base 1.0
- bam_aux2Z at Base 1.0
- bam_aux2f at Base 1.0
- bam_aux2i at Base 1.0
- bam_auxB2f at Base 1.4.1
- bam_auxB2i at Base 1.4.1
- bam_auxB_len at Base 1.4.1
- bam_aux_append at Base 1.0
- bam_aux_del at Base 1.0
- bam_aux_get at Base 1.0
- bam_aux_update_str at Base 1.4.1
- bam_cigar2qlen at Base 1.0
- bam_cigar2rlen at Base 1.0
- bam_construct_seq at Base 1.0
- bam_copy1 at Base 1.0
- bam_destroy1 at Base 1.0
- bam_dup1 at Base 1.0
- bam_endpos at Base 1.0
- bam_flag2str at Base 1.0
- bam_hdr_destroy at Base 1.0
- bam_hdr_dup at Base 1.0
- bam_hdr_init at Base 1.0
- bam_hdr_read at Base 1.0
- bam_hdr_write at Base 1.0
- bam_header_to_cram at Base 1.0
- bam_index_build at Base 1.0
- bam_init1 at Base 1.0
- bam_mplp_auto at Base 1.0
- bam_mplp_constructor at Base 1.4.1
- bam_mplp_destroy at Base 1.0
- bam_mplp_destructor at Base 1.4.1
- bam_mplp_init at Base 1.0
- bam_mplp_init_overlaps at Base 1.0
- bam_mplp_reset at Base 1.4.1
- bam_mplp_set_maxcnt at Base 1.0
- bam_name2id at Base 1.0
- bam_plp_auto at Base 1.0
- bam_plp_constructor at Base 1.4.1
- bam_plp_destroy at Base 1.0
- bam_plp_destructor at Base 1.4.1
- bam_plp_init at Base 1.0
- bam_plp_init_overlaps at Base 1.0
- bam_plp_next at Base 1.0
- bam_plp_push at Base 1.0
- bam_plp_reset at Base 1.0
- bam_plp_set_maxcnt at Base 1.0
- bam_read1 at Base 1.0
- bam_str2flag at Base 1.0
- bam_write1 at Base 1.0
- bcf_add_filter at Base 1.0
- bcf_add_id at Base 1.3
- bcf_calc_ac at Base 1.0
- bcf_clear at Base 1.0
- bcf_copy at Base 1.2.1
- bcf_destroy at Base 1.0
- bcf_dup at Base 1.0
- bcf_empty at Base 1.3
- bcf_enc_vchar at Base 1.0
- bcf_enc_vfloat at Base 1.0
- bcf_enc_vint at Base 1.0
- bcf_float_missing at Base 1.0
- bcf_float_vector_end at Base 1.0
- bcf_fmt_array at Base 1.0
- bcf_fmt_sized_array at Base 1.0
- bcf_get_fmt at Base 1.0
- bcf_get_fmt_id at Base 1.1
- bcf_get_format_string at Base 1.0
- bcf_get_format_values at Base 1.0
- bcf_get_info at Base 1.0
- bcf_get_info_id at Base 1.1
- bcf_get_info_values at Base 1.0
- bcf_get_variant_type at Base 1.0
- bcf_get_variant_types at Base 1.0
- bcf_gt_type at Base 1.0
- bcf_has_filter at Base 1.0
- bcf_hdr_add_hrec at Base 1.0
- bcf_hdr_add_sample at Base 1.0
- bcf_hdr_append at Base 1.0
- bcf_hdr_check_sanity at Base 1.0
- bcf_hdr_combine at Base 1.0
- bcf_hdr_destroy at Base 1.0
- bcf_hdr_dup at Base 1.0
- bcf_hdr_fmt_text at Base 1.0
- bcf_hdr_format at Base 1.4.1
- bcf_hdr_get_hrec at Base 1.0
- bcf_hdr_get_version at Base 1.0
- bcf_hdr_id2int at Base 1.0
- bcf_hdr_init at Base 1.0
- bcf_hdr_merge at Base 1.3
- bcf_hdr_parse at Base 1.0
- bcf_hdr_parse_line at Base 1.0
- bcf_hdr_parse_sample_line at Base 1.0
- bcf_hdr_printf at Base 1.0
- bcf_hdr_read at Base 1.0
- bcf_hdr_register_hrec at Base 1.0
- bcf_hdr_remove at Base 1.0
- bcf_hdr_seqnames at Base 1.0
- bcf_hdr_set at Base 1.0
- bcf_hdr_set_samples at Base 1.0
- bcf_hdr_set_version at Base 1.0
- bcf_hdr_subset at Base 1.0
- bcf_hdr_sync at Base 1.0
- bcf_hdr_write at Base 1.0
- bcf_header_debug at Base 1.0
- bcf_hrec_add_key at Base 1.0
- bcf_hrec_debug at Base 1.0
- bcf_hrec_destroy at Base 1.0
- bcf_hrec_dup at Base 1.0
- bcf_hrec_find_key at Base 1.0
- bcf_hrec_format at Base 1.0
- bcf_hrec_set_val at Base 1.0
- bcf_index at Base 1.0
- bcf_index_build2 at Base 1.3
- bcf_index_build3 at Base 1.4.1
- bcf_index_build at Base 1.0
- bcf_index_load2 at Base 1.3
- bcf_init at Base 1.0
- bcf_is_snp at Base 1.0
- bcf_read at Base 1.0
- bcf_readrec at Base 1.0
- bcf_remove_allele_set at Base 1.3
- bcf_remove_alleles at Base 1.0
- bcf_remove_filter at Base 1.0
- bcf_sr_add_reader at Base 1.0
- bcf_sr_destroy at Base 1.0
- bcf_sr_destroy_threads at Base 1.4.1
- bcf_sr_init at Base 1.0
- bcf_sr_next_line at Base 1.0
- bcf_sr_regions_destroy at Base 1.0
- bcf_sr_regions_flush at Base 1.0
- bcf_sr_regions_init at Base 1.0
- bcf_sr_regions_next at Base 1.0
- bcf_sr_regions_overlap at Base 1.0
- bcf_sr_regions_seek at Base 1.0
- bcf_sr_remove_reader at Base 1.0
- bcf_sr_seek at Base 1.0
- bcf_sr_set_opt at Base 1.4.1
- bcf_sr_set_regions at Base 1.0
- bcf_sr_set_samples at Base 1.0
- bcf_sr_set_targets at Base 1.0
- bcf_sr_set_threads at Base 1.4.1
- bcf_sr_sort_destroy at Base 1.4.1
- bcf_sr_sort_init at Base 1.4.1
- bcf_sr_sort_next at Base 1.4.1
- bcf_sr_sort_remove_reader at Base 1.4.1
- bcf_sr_strerror at Base 1.2.1
- bcf_subset at Base 1.0
- bcf_subset_format at Base 1.0
- bcf_sweep_bwd at Base 1.0
- bcf_sweep_destroy at Base 1.0
- bcf_sweep_fwd at Base 1.0
- bcf_sweep_hdr at Base 1.0
- bcf_sweep_init at Base 1.0
- bcf_translate at Base 1.0
- bcf_trim_alleles at Base 1.0
- bcf_type_shift at Base 1.0
- bcf_unpack at Base 1.0
- bcf_update_alleles at Base 1.0
- bcf_update_alleles_str at Base 1.0
- bcf_update_filter at Base 1.0
- bcf_update_format at Base 1.0
- bcf_update_format_string at Base 1.0
- bcf_update_id at Base 1.0
- bcf_update_info at Base 1.0
- bcf_write at Base 1.0
- bgzf_block_write at Base 1.4.1
- bgzf_check_EOF at Base 1.0
- bgzf_close at Base 1.0
- bgzf_compress at Base 1.3
- bgzf_compression at Base 1.4.1
- bgzf_decode_func at Base 1.4.1
- bgzf_dopen at Base 1.0
- bgzf_encode_func at Base 1.4.1
- bgzf_flush at Base 1.0
- bgzf_flush_try at Base 1.0
- bgzf_getc at Base 1.0
- bgzf_getline at Base 1.0
- bgzf_hfile at Base 1.5
- bgzf_hopen at Base 1.0
- bgzf_index_add_block at Base 1.0
- bgzf_index_build_init at Base 1.0
- bgzf_index_destroy at Base 1.0
- bgzf_index_dump at Base 1.0
- bgzf_index_dump_hfile at Base 1.4.1
- bgzf_index_load at Base 1.0
- bgzf_index_load_hfile at Base 1.4.1
- bgzf_is_bgzf at Base 1.0
- bgzf_mt at Base 1.0
- bgzf_mt_read_block at Base 1.4.1
- bgzf_nul_func at Base 1.4.1
- bgzf_open at Base 1.0
- bgzf_raw_read at Base 1.0
- bgzf_raw_write at Base 1.0
- bgzf_read at Base 1.0
- bgzf_read_block at Base 1.0
- bgzf_seek at Base 1.0
- bgzf_set_cache_size at Base 1.0
- bgzf_thread_pool at Base 1.4.1
- bgzf_useek at Base 1.0
- bgzf_utell at Base 1.0
- bgzf_write at Base 1.0
- cram_beta_decode_char at Base 1.0
- cram_beta_decode_free at Base 1.0
- cram_beta_decode_init at Base 1.0
- cram_beta_decode_int at Base 1.0
- cram_beta_encode_char at Base 1.0
- cram_beta_encode_free at Base 1.0
- cram_beta_encode_init at Base 1.0
- cram_beta_encode_int at Base 1.0
- cram_beta_encode_store at Base 1.0
- cram_block_append at Base 1.3
- cram_block_compression_hdr_decoder2encoder at Base 1.3
- cram_block_compression_hdr_set_rg at Base 1.3
- cram_block_get_comp_size at Base 1.3
- cram_block_get_content_id at Base 1.3
- cram_block_get_content_type at Base 1.3
- cram_block_get_crc32 at Base 1.3
- cram_block_get_data at Base 1.3
- cram_block_get_offset at Base 1.3
- cram_block_get_size at Base 1.3
- cram_block_get_uncomp_size at Base 1.3
- cram_block_method2str at Base 1.0
- cram_block_set_comp_size at Base 1.3
- cram_block_set_content_id at Base 1.3
- cram_block_set_crc32 at Base 1.3
- cram_block_set_data at Base 1.3
- cram_block_set_offset at Base 1.3
- cram_block_set_size at Base 1.3
- cram_block_set_uncomp_size at Base 1.3
- cram_block_size at Base 1.3
- cram_block_update_size at Base 1.3
- cram_byte_array_len_decode at Base 1.0
- cram_byte_array_len_decode_free at Base 1.0
- cram_byte_array_len_decode_init at Base 1.0
- cram_byte_array_len_encode at Base 1.0
- cram_byte_array_len_encode_free at Base 1.0
- cram_byte_array_len_encode_init at Base 1.0
- cram_byte_array_len_encode_store at Base 1.0
- cram_byte_array_stop_decode_block at Base 1.0
- cram_byte_array_stop_decode_free at Base 1.0
- cram_byte_array_stop_decode_init at Base 1.0
- cram_byte_array_stop_encode at Base 1.0
- cram_byte_array_stop_encode_free at Base 1.0
- cram_byte_array_stop_encode_init at Base 1.0
- cram_byte_array_stop_encode_store at Base 1.0
- cram_check_EOF at Base 1.4.1
- cram_close at Base 1.0
- cram_codec_decoder2encoder at Base 1.3
- cram_codec_to_id at Base 1.2.1
- cram_compress_block at Base 1.0
- cram_container_get_landmarks at Base 1.3
- cram_container_get_length at Base 1.3
- cram_container_get_num_blocks at Base 1.3
- cram_container_is_empty at Base 1.3
- cram_container_set_landmarks at Base 1.3
- cram_container_set_length at Base 1.3
- cram_container_set_num_blocks at Base 1.3
- cram_container_size at Base 1.3
- cram_content_type2str at Base 1.0
- cram_copy_slice at Base 1.3
- cram_decode_TD at Base 1.0
- cram_decode_compression_header at Base 1.0
- cram_decode_estimate_sizes at Base 1.3
- cram_decode_slice at Base 1.0
- cram_decode_slice_header at Base 1.0
- cram_decode_slice_mt at Base 1.0
- cram_decode_slice_thread at Base 1.0
- cram_decoder_init at Base 1.0
- cram_dependent_data_series at Base 1.2.1
- cram_dopen at Base 1.0
- cram_encode_compression_header at Base 1.0
- cram_encode_container at Base 1.0
- cram_encode_slice_header at Base 1.0
- cram_encoder_init at Base 1.0
- cram_encoding2str at Base 1.0
- cram_eof at Base 1.0
- cram_external_decode_char at Base 1.0
- cram_external_decode_free at Base 1.0
- cram_external_decode_init at Base 1.0
- cram_external_decode_int at Base 1.0
- cram_external_encode_char at Base 1.2.1
- cram_external_encode_free at Base 1.0
- cram_external_encode_init at Base 1.0
- cram_external_encode_int at Base 1.2.1
- cram_external_encode_store at Base 1.0
- cram_fd_get_fp at Base 1.3
- cram_fd_get_header at Base 1.3
- cram_fd_get_version at Base 1.3
- cram_fd_set_fp at Base 1.3
- cram_fd_set_header at Base 1.3
- cram_fd_set_version at Base 1.3
- cram_flush at Base 1.0
- cram_flush_container at Base 1.0
- cram_flush_container_mt at Base 1.0
- cram_flush_thread at Base 1.0
- cram_free_block at Base 1.0
- cram_free_compression_header at Base 1.0
- cram_free_container at Base 1.0
- cram_free_file_def at Base 1.0
- cram_free_slice at Base 1.0
- cram_free_slice_header at Base 1.0
- cram_gamma_decode at Base 1.0
- cram_gamma_decode_free at Base 1.0
- cram_gamma_decode_init at Base 1.0
- cram_get_bam_seq at Base 1.0
- cram_get_ref at Base 1.0
- cram_get_refs at Base 1.4.1
- cram_get_seq at Base 1.0
- cram_header_to_bam at Base 1.0
- cram_huffman_decode_char0 at Base 1.0
- cram_huffman_decode_char at Base 1.0
- cram_huffman_decode_free at Base 1.0
- cram_huffman_decode_init at Base 1.0
- cram_huffman_decode_int0 at Base 1.0
- cram_huffman_decode_int at Base 1.0
- cram_huffman_decode_null at Base 1.3
- cram_huffman_encode_char0 at Base 1.0
- cram_huffman_encode_char at Base 1.0
- cram_huffman_encode_free at Base 1.0
- cram_huffman_encode_init at Base 1.0
- cram_huffman_encode_int0 at Base 1.0
- cram_huffman_encode_int at Base 1.0
- cram_huffman_encode_store at Base 1.0
- cram_index_build at Base 1.0
- cram_index_free at Base 1.0
- cram_index_load at Base 1.0
- cram_index_query at Base 1.0
- cram_load_reference at Base 1.0
- cram_major_vers at Base 1.3
- cram_minor_vers at Base 1.3
- cram_new_block at Base 1.0
- cram_new_compression_header at Base 1.0
- cram_new_container at Base 1.0
- cram_new_metrics at Base 1.0
- cram_new_slice at Base 1.0
- cram_nop_decode_reset at Base 1.4.1
- cram_open at Base 1.0
- cram_put_bam_seq at Base 1.0
- cram_read_SAM_hdr at Base 1.0
- cram_read_block at Base 1.0
- cram_read_container at Base 1.0
- cram_read_file_def at Base 1.0
- cram_read_slice at Base 1.0
- cram_ref_decr at Base 1.0
- cram_ref_incr at Base 1.0
- cram_ref_load at Base 1.0
- cram_seek at Base 1.0
- cram_seek_to_refpos at Base 1.0
- cram_set_header at Base 1.0
- cram_set_option at Base 1.0
- cram_set_voption at Base 1.0
- cram_slice_hdr_get_num_blocks at Base 1.3
- cram_stats_add at Base 1.0
- cram_stats_create at Base 1.0
- cram_stats_del at Base 1.0
- cram_stats_dump at Base 1.0
- cram_stats_encoding at Base 1.0
- cram_stats_free at Base 1.0
- cram_store_container at Base 1.3
- cram_subexp_decode at Base 1.0
- cram_subexp_decode_free at Base 1.0
- cram_subexp_decode_init at Base 1.0
- cram_to_bam at Base 1.4.1
- cram_transcode_rg at Base 1.3
- cram_uncompress_block at Base 1.0
- cram_update_curr_slice at Base 1.4.1
- cram_write_SAM_hdr at Base 1.0
- cram_write_block at Base 1.0
- cram_write_container at Base 1.0
- cram_write_file_def at Base 1.0
- debug_buffer at Base 1.0
- debug_buffers at Base 1.0
- debug_vbuf at Base 1.4.1
- debug_vsets at Base 1.4.1
- errmod_cal at Base 1.4.1
- errmod_destroy at Base 1.4.1
- errmod_init at Base 1.4.1
- expand_cache_path at Base 1.0
- fai_build3 at Base 1.4.1
- fai_build at Base 1.0
- fai_build_core at Base 1.0
- fai_destroy at Base 1.0
- fai_fetch at Base 1.0
- fai_load3 at Base 1.4.1
- fai_load at Base 1.0
- faidx_fetch_nseq at Base 1.2.1
- faidx_fetch_seq at Base 1.0
- faidx_has_seq at Base 1.0
- faidx_iseq at Base 1.1
- faidx_nseq at Base 1.1
- faidx_seq_len at Base 1.1
- file_exists at Base 1.0
- file_size at Base 1.0
- find_file_url at Base 1.0
- find_path at Base 1.3
- grp_create_key at Base 1.4.1
- hclose at Base 1.0
- hclose_abruptly at Base 1.0
- hdopen at Base 1.0
- hfile_add_scheme_handler at Base 1.3
- hfile_always_local at Base 1.3
- hfile_always_remote at Base 1.3
- hfile_destroy at Base 1.0
- hfile_init at Base 1.0
- hfile_init_fixed at Base 1.4.1
- hfile_oflags at Base 1.0
- hfile_plugin_init_gcs at Base 1.4.1
- hfile_plugin_init_libcurl at Base 1.3.1
- hfile_plugin_init_net at Base 1.3
- hfile_plugin_init_s3 at Base 1.4.1
- hfile_set_blksize at Base 1.5
- hflush at Base 1.0
- hgetc2 at Base 1.0
- hgetdelim at Base 1.4.1
- hgets at Base 1.4.1
- hisremote at Base 1.2.1
- hopen at Base 1.0
- hopen_json_redirect at Base 1.4.1
- hopen_net at Base 1.0
- hpeek at Base 1.0
- hputc2 at Base 1.0
- hputs2 at Base 1.0
- hread2 at Base 1.0
- hrec_add_idx at Base 1.0
- hseek at Base 1.0
- hts_base64_decoded_length at Base 1.4.1
- hts_check_EOF at Base 1.4.1
- hts_close at Base 1.0
- hts_decode_base64 at Base 1.4.1
- hts_decode_percent at Base 1.4.1
- hts_detect_format at Base 1.2.1
- hts_file_type at Base 1.0
- hts_format_description at Base 1.2.1
- hts_format_file_extension at Base 1.3
- hts_get_bgzfp at Base 1.0
- hts_get_format at Base 1.2.1
- hts_get_log_level at Base 1.5
- hts_getline at Base 1.0
- hts_hopen at Base 1.2.1
- hts_idx_destroy at Base 1.0
- hts_idx_finish at Base 1.0
- hts_idx_get_meta at Base 1.0
- hts_idx_get_n_no_coor at Base 1.0
- hts_idx_get_stat at Base 1.0
- hts_idx_getfn at Base 1.0
- hts_idx_init at Base 1.0
- hts_idx_load2 at Base 1.3
- hts_idx_load at Base 1.0
- hts_idx_push at Base 1.0
- hts_idx_save at Base 1.0
- hts_idx_save_as at Base 1.3
- hts_idx_seqnames at Base 1.0
- hts_idx_set_meta at Base 1.0
- hts_itr_destroy at Base 1.0
- hts_itr_next at Base 1.0
- hts_itr_query at Base 1.0
- hts_itr_querys at Base 1.0
- hts_json_fnext at Base 1.4.1
- hts_json_fskip_value at Base 1.4.1
- hts_json_snext at Base 1.4.1
- hts_json_sskip_value at Base 1.4.1
- hts_log at Base 1.5
- hts_md5_destroy at Base 1.3
- hts_md5_final at Base 1.3
- hts_md5_hex at Base 1.3
- hts_md5_init at Base 1.3
- hts_md5_reset at Base 1.3
- hts_md5_update at Base 1.3
- hts_open at Base 1.0
- hts_open_format at Base 1.3
- hts_opt_add at Base 1.3
- hts_opt_apply at Base 1.3
- hts_opt_free at Base 1.3
- hts_parse_decimal at Base 1.3
- hts_parse_format at Base 1.3
- hts_parse_opt_list at Base 1.3
- hts_parse_reg at Base 1.0
- hts_readlines at Base 1.0
- hts_readlist at Base 1.0
- hts_realloc_or_die at Base 1.4.1
- hts_set_cache_size at Base 1.4.1
- hts_set_fai_filename at Base 1.0
- hts_set_log_level at Base 1.5
- hts_set_opt at Base 1.2.1
- hts_set_thread_pool at Base 1.4.1
- hts_set_threads at Base 1.0
- hts_tpool_delete_result at Base 1.4.1
- hts_tpool_destroy at Base 1.4.1
- hts_tpool_dispatch2 at Base 1.4.1
- hts_tpool_dispatch at Base 1.4.1
- hts_tpool_init at Base 1.4.1
- hts_tpool_kill at Base 1.4.1
- hts_tpool_next_result at Base 1.4.1
- hts_tpool_next_result_wait at Base 1.4.1
- hts_tpool_process_attach at Base 1.4.1
- hts_tpool_process_destroy at Base 1.4.1
- hts_tpool_process_detach at Base 1.4.1
- hts_tpool_process_empty at Base 1.4.1
- hts_tpool_process_flush at Base 1.4.1
- hts_tpool_process_init at Base 1.4.1
- hts_tpool_process_len at Base 1.4.1
- hts_tpool_process_qsize at Base 1.4.1
- hts_tpool_process_ref_decr at Base 1.4.1
- hts_tpool_process_ref_incr at Base 1.4.1
- hts_tpool_process_reset at Base 1.4.1
- hts_tpool_process_shutdown at Base 1.4.1
- hts_tpool_process_sz at Base 1.4.1
- hts_tpool_result_data at Base 1.4.1
- hts_tpool_size at Base 1.4.1
- hts_tpool_wake_dispatch at Base 1.4.1
- hts_useek at Base 1.0
- hts_utell at Base 1.0
- hts_verbose at Base 1.0
- hts_version at Base 1.0
- hwrite2 at Base 1.0
- int32_decode at Base 1.0
- int32_encode at Base 1.0
- int32_get_blk at Base 1.3
- int32_put_blk at Base 1.3
- is_directory at Base 1.0
- is_file at Base 1.0
- itf8_bytes at Base 1.3
- itf8_decode at Base 1.0
- itf8_decode_crc at Base 1.3
- itf8_encode at Base 1.0
- itf8_put_blk at Base 1.0
- kf_betai at Base 1.0
- kf_erfc at Base 1.0
- kf_gammap at Base 1.0
- kf_gammaq at Base 1.0
- kf_lgamma at Base 1.0
- kftp_connect at Base 1.0
- kftp_connect_file at Base 1.0
- kftp_parse_url at Base 1.0
- kftp_reconnect at Base 1.0
- kgetline at Base 1.3
- kh_clear_s2i at Base 1.0
- kh_del_s2i at Base 1.0
- kh_destroy_s2i at Base 1.0
- kh_get_s2i at Base 1.0
- kh_init_s2i at Base 1.0
- kh_put_s2i at Base 1.0
- kh_resize_s2i at Base 1.0
- khttp_connect_file at Base 1.0
- khttp_parse_url at Base 1.0
- kmemmem at Base 1.0
- knet_close at Base 1.0
- knet_dopen at Base 1.0
- knet_open at Base 1.0
- knet_read at Base 1.0
- knet_seek at Base 1.0
- kputd at Base 1.4.1
- ks_combsort__off at Base 1.0
- ks_combsort_uint16_t at Base 1.4.1
- ks_heapadjust__off at Base 1.0
- ks_heapadjust_uint16_t at Base 1.4.1
- ks_heapmake__off at Base 1.0
- ks_heapmake_uint16_t at Base 1.4.1
- ks_heapsort__off at Base 1.0
- ks_heapsort_uint16_t at Base 1.4.1
- ks_introsort__off at Base 1.0
- ks_introsort_uint16_t at Base 1.4.1
- ks_ksmall__off at Base 1.0
- ks_ksmall_uint16_t at Base 1.4.1
- ks_mergesort__off at Base 1.0
- ks_mergesort_uint16_t at Base 1.4.1
- ks_shuffle__off at Base 1.0
- ks_shuffle_uint16_t at Base 1.4.1
- ksplit_core at Base 1.0
- ksprintf at Base 1.0
- kstrnstr at Base 1.0
- kstrstr at Base 1.0
- kstrtok at Base 1.0
- kt_fisher_exact at Base 1.0
- kvsprintf at Base 1.0
- ltf8_bytes at Base 1.4.1
- ltf8_decode at Base 1.0
- ltf8_decode_crc at Base 1.3
- merge_vsets at Base 1.4.1
- mfascii at Base 1.0
- mfclose at Base 1.0
- mfcreate at Base 1.0
- mfcreate_from at Base 1.0
- mfdestroy at Base 1.0
- mfdetach at Base 1.0
- mfeof at Base 1.0
- mfflush at Base 1.0
- mfgetc at Base 1.0
- mfgets at Base 1.0
- mfmmap at Base 1.3
- mfopen at Base 1.0
- mfread at Base 1.0
- mfrecreate at Base 1.0
- mfreopen at Base 1.0
- mfseek at Base 1.0
- mfsteal at Base 1.0
- mftell at Base 1.0
- mftruncate at Base 1.0
- mfwrite at Base 1.0
- mkdir_prefix at Base 1.0
- mrewind at Base 1.0
- mstderr at Base 1.0
- mstdin at Base 1.0
- mstdout at Base 1.0
- mungetc at Base 1.0
- open_path_mfile at Base 1.0
- pairing_score at Base 1.4.1
- pool_alloc at Base 1.0
- pool_create at Base 1.0
- pool_destroy at Base 1.0
- pool_free at Base 1.0
- probaln_glocal at Base 1.4.1
- push_vset at Base 1.4.1
- rans_compress at Base 1.2.1
- rans_compress_O0 at Base 1.2.1
- rans_compress_O1 at Base 1.2.1
- rans_uncompress at Base 1.2.1
- rans_uncompress_O0 at Base 1.2.1
- rans_uncompress_O1 at Base 1.2.1
- refs2id at Base 1.0
- refs_free at Base 1.0
- regidx_destroy at Base 1.2.1
- regidx_init at Base 1.2.1
- regidx_insert at Base 1.2.1
- regidx_nregs at Base 1.2.1
- regidx_overlap at Base 1.2.1
- regidx_parse_bed at Base 1.2.1
- regidx_parse_tab at Base 1.2.1
- regidx_seq_names at Base 1.2.1
- regidx_seq_nregs at Base 1.2.1
- remove_vset at Base 1.4.1
- sam_cap_mapq at Base 1.4.1
- sam_format1 at Base 1.0
- sam_hdr_PG_ID at Base 1.0
- sam_hdr_add at Base 1.0
- sam_hdr_add_PG at Base 1.0
- sam_hdr_add_lines at Base 1.0
- sam_hdr_decr_ref at Base 1.0
- sam_hdr_dump at Base 1.0
- sam_hdr_dup at Base 1.0
- sam_hdr_find at Base 1.0
- sam_hdr_find_key at Base 1.0
- sam_hdr_find_line at Base 1.0
- sam_hdr_find_rg at Base 1.0
- sam_hdr_free at Base 1.0
- sam_hdr_incr_ref at Base 1.0
- sam_hdr_length at Base 1.0
- sam_hdr_link_pg at Base 1.0
- sam_hdr_name2ref at Base 1.0
- sam_hdr_new at Base 1.0
- sam_hdr_parse at Base 1.0
- sam_hdr_parse_ at Base 1.0
- sam_hdr_read at Base 1.0
- sam_hdr_rebuild at Base 1.0
- sam_hdr_sort_order at Base 1.3
- sam_hdr_str at Base 1.0
- sam_hdr_update at Base 1.0
- sam_hdr_vadd at Base 1.0
- sam_hdr_write at Base 1.0
- sam_index_build2 at Base 1.3
- sam_index_build3 at Base 1.4.1
- sam_index_build at Base 1.3
- sam_index_load2 at Base 1.3
- sam_index_load at Base 1.0
- sam_itr_queryi at Base 1.0
- sam_itr_querys at Base 1.0
- sam_open_mode at Base 1.0
- sam_open_mode_opts at Base 1.3
- sam_parse1 at Base 1.0
- sam_prob_realn at Base 1.4.1
- sam_read1 at Base 1.0
- sam_write1 at Base 1.0
- seq_nt16_int at Base 1.2.1
- seq_nt16_str at Base 1.0
- seq_nt16_table at Base 1.0
- string_alloc at Base 1.0
- string_dup at Base 1.0
- string_ndup at Base 1.0
- string_pool_create at Base 1.0
- string_pool_destroy at Base 1.0
- stringify_argv at Base 1.0
- tbx_conf_bed at Base 1.0
- tbx_conf_gff at Base 1.0
- tbx_conf_psltbl at Base 1.0
- tbx_conf_sam at Base 1.0
- tbx_conf_vcf at Base 1.0
- tbx_destroy at Base 1.0
- tbx_index at Base 1.0
- tbx_index_build2 at Base 1.3
- tbx_index_build3 at Base 1.4.1
- tbx_index_build at Base 1.0
- tbx_index_load2 at Base 1.3
- tbx_index_load at Base 1.0
- tbx_name2id at Base 1.0
- tbx_parse1 at Base 1.0
- tbx_readrec at Base 1.0
- tbx_seqnames at Base 1.0
- tbx_set_meta at Base 1.0
- tokenise_search_path at Base 1.0
- vcf_format at Base 1.0
- vcf_hdr_read at Base 1.0
- vcf_hdr_write at Base 1.0
- vcf_parse at Base 1.0
- vcf_read at Base 1.0
- vcf_write at Base 1.0
- vcf_write_line at Base 1.0
- zlib_mem_inflate at Base 1.0
diff --git a/debian/patches/877670.patch b/debian/patches/877670.patch
deleted file mode 100644
index 82f9f09..0000000
--- a/debian/patches/877670.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Description: Fix calculation of PLs on ARM and POWER
-Bug: https://github.com/samtools/bcftools/issues/702
-Bug-Debian: https://bugs.debian.org/877670
-Forwarded: https://github.com/samtools/htslib/pull/617
-Applied-Upstream: https://github.com/samtools/htslib/commit/829ddaea433cd55cc5bd9a6d38ec6d9593ad50b4
-Author: Graham Inggs <ginggs at debian.org>
-Last-Update: 2017-11-10
---- a/errmod.c
-+++ b/errmod.c
-@@ -62,7 +62,7 @@
- static void cal_coef(errmod_t *em, double depcorr, double eta)
- {
- int k, n, q;
-- long double sum, sum1;
-+ double sum, sum1;
- double *lC;
-
- // initialize ->fk
-@@ -82,10 +82,11 @@
- double le1 = log(1.0 - e);
- for (n = 1; n <= 255; ++n) {
- double *beta = em->beta + (q<<16|n<<8);
-- sum1 = sum = 0.0;
-- for (k = n; k >= 0; --k, sum1 = sum) {
-- sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1);
-- beta[k] = -10. / M_LN10 * logl(sum1 / sum);
-+ sum1 = lC[n<<8|n] + n*le;
-+ beta[n] = HUGE_VAL;
-+ for (k = n - 1; k >= 0; --k, sum1 = sum) {
-+ sum = sum1 + log1p(exp(lC[n<<8|k] + k*le + (n-k)*le1 - sum1));
-+ beta[k] = -10. / M_LN10 * (sum1 - sum);
- }
- }
- }
diff --git a/debian/patches/define_PATH_MAX.patch b/debian/patches/define_PATH_MAX.patch
deleted file mode 100644
index 9687d33..0000000
--- a/debian/patches/define_PATH_MAX.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-Author: Andreas Tille <tille at debian.org>,
- Svante Signell <svante.signell at gmail.com>
-Last-Uudate: Wed, 31 Aug 2016 12:14:45 +0200
-Bug-Debian: https://bugs.debian.org/793512
- https://bugs.debian.org/836190
-Description: Define PATH_MAX as it is done in cram/open_trace_file.c if
- not existent. The definition should be removed from this C file since the
- header file affects all three C files where this definition is used.
-
---- a/cram/os.h
-+++ b/cram/os.h
-@@ -159,6 +159,13 @@ static inline uint16_t le_int2(uint16_t
- }
- #endif
-
-+/*
-+ * in case PATH_MAX is not defined (like in hurd)
-+ */
-+#ifndef PATH_MAX
-+# define PATH_MAX 1024
-+#endif
-+
- /*-----------------------------------------------------------------------------
- * <inttypes.h> definitions, incase they're not present
- */
---- a/cram/open_trace_file.c
-+++ b/cram/open_trace_file.c
-@@ -71,9 +71,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- #include <sys/types.h>
- #include <sys/stat.h>
- #include "cram/os.h"
--#ifndef PATH_MAX
--# define PATH_MAX 1024
--#endif
-
- #include "cram/open_trace_file.h"
- #include "cram/misc.h"
diff --git a/debian/patches/fPIC.patch b/debian/patches/fPIC.patch
deleted file mode 100644
index d2b7cd3..0000000
--- a/debian/patches/fPIC.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: Build with -fPIC instead of -fpic
- It doesn't make a difference on x86, but is required for
- linking the library on s390x and sparc64.
-Author: Adrian Bunk <bunk at debian.org>
-
---- htslib-1.4.1.orig/Makefile
-+++ htslib-1.4.1/Makefile
-@@ -34,7 +34,7 @@ CPPFLAGS =
- # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
- #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
- CFLAGS = -g -Wall -O2
--EXTRA_CFLAGS_PIC = -fpic
-+EXTRA_CFLAGS_PIC = -fPIC
- LDFLAGS =
- LIBS = $(htslib_default_libs)
-
diff --git a/debian/patches/fix_pkg-config.patch b/debian/patches/fix_pkg-config.patch
deleted file mode 100644
index fd77d1c..0000000
--- a/debian/patches/fix_pkg-config.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Description: This patch is deactivated
- --> see https://bugs.debian.org/881170
- debian/patches/fix_pkg-config.patch is incorrect
- .
- Cflags are just pointing to system default include dir. However, files are in
- subdirectory which cram/*.h input files are kept in. To be found pkg-config
- needs to point to this dir
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 09 Feb 2017 13:39:57 +0100
-
---- a/htslib.pc.in
-+++ b/htslib.pc.in
-@@ -9,7 +9,7 @@ static_libs=@static_LIBS@
- Name: htslib
- Description: C library for high-throughput sequencing data formats
- Version: @-PACKAGE_VERSION@
--Cflags: -I${includedir}
-+Cflags: -I${includedir}/htslib
- Libs: -L${libdir} -lhts
- Libs.private: -L${libdir} @private_LIBS@ -lhts -lm -lpthread
- Requires.private: zlib @pc_requires@
diff --git a/debian/patches/htslib-add-cram_to_bam.patch b/debian/patches/htslib-add-cram_to_bam.patch
deleted file mode 100644
index 3cb6ba7..0000000
--- a/debian/patches/htslib-add-cram_to_bam.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Description: This patch adds the cram_to_bam function to the public interface of htslib,
- because it is used by code in Sambamba.
-Author: Roel Janssen <roel at gnu.org>
-Last-Update: 3 May 2016
-Origin: https://github.com/UMCUGenetics/guix-additions/blob/master/htslib-add-cram_to_bam.patch
-
---- a/cram/cram_decode.c
-+++ b/cram/cram_decode.c
-@@ -2825,7 +2825,7 @@ int cram_decode_slice_mt(cram_fd *fd, cr
- * Returns the used size of the bam record on success
- * -1 on failure.
- */
--static int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
-+int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
- cram_record *cr, int rec, bam_seq_t **bam) {
- int bam_idx, rg_len;
- char name_a[1024], *name;
---- a/cram/cram_decode.h
-+++ b/cram/cram_decode.h
-@@ -104,6 +104,8 @@ cram_block_slice_hdr *cram_decode_slice_
- int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
- SAM_hdr *hdr);
-
-+int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
-+ cram_record *cr, int rec, bam_seq_t **bam);
-
- #ifdef __cplusplus
- }
diff --git a/debian/patches/literal_version.patch b/debian/patches/literal_version.patch
deleted file mode 100644
index be9c8e2..0000000
--- a/debian/patches/literal_version.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: do not use make to extract version
- Without a valid config.mk, trying to call m4_esyscmd_s() to run
- make results in weird error messages. This patch avoids having
- to run make just to extract this value.
-Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/configure.ac
-+++ b/configure.ac
-@@ -23,7 +23,7 @@
- # DEALINGS IN THE SOFTWARE.
-
- dnl Process this file with autoconf to produce a configure script
--AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
-+AC_INIT([HTSlib], m4_esyscmd_s([grep 'PACKAGE_VERSION =' Makefile | cut -f 2 -d'=' | xargs]),
- [samtools-help at lists.sourceforge.net], [], [http://www.htslib.org/])
- AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER
- AC_CONFIG_SRCDIR(hts.c)
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index b6dad30..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,5 +0,0 @@
-define_PATH_MAX.patch
-literal_version.patch
-htslib-add-cram_to_bam.patch
-fPIC.patch
-877670.patch
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index e735b5f..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/make -f
-
-# export DEB_BUILD_MAINT_OPTIONS = hardening=+all # Build fails due to -fpie
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-
-export DH_VERBOSE=1
-
-include /usr/share/dpkg/default.mk
-
-ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))
- export DEB_CFLAGS_MAINT_APPEND=-fno-strict-aliasing -fno-code-hoisting
-endif
-
-%:
- dh $@
-
-override_dh_auto_test:
- dh_auto_test
- $(RM) test/*.tmp test/*.tmp.* test/*.o test/*.dSYM \
- test/fieldarith test/hfile test/test_view test/test-vcf-api test/test-vcf-sweep
-
-override_dh_auto_configure:
- autoconf
- dh_auto_configure -- --enable-libcurl
-
-override_dh_auto_build:
- dh_auto_build -- \
- CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \
- CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \
-# re-try later LDLIBS=-lhts \
- PACKAGE_VERSION="$(DEB_VERSION)" \
- libdir=/usr/lib/$(DEB_HOST_MULTIARCH)
-
-override_dh_auto_install:
- for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \
- rm $(CURDIR)/test/$${binary} ; \
- done
- dh_auto_install -- \
- prefix=/usr \
- libdir=/usr/lib/$(DEB_HOST_MULTIARCH) \
- PACKAGE_VERSION="$(DEB_VERSION)"
-
-override_dh_installchangelogs:
- dh_installchangelogs NEWS
-
-override_dh_link-indep:
- dh_link -i
- # provide header files as expected by the Makefile of the test suite via symlinks
- for l in `ls debian/libhts-dev/usr/include/htslib/cram/*.h` ; do \
- ln -s ../../../include/htslib/cram/`basename $$l` $(CURDIR)/debian/htslib-test/usr/share/htslib-test/cram/ ; \
- done
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/source/options b/debian/source/options
deleted file mode 100644
index 9511377..0000000
--- a/debian/source/options
+++ /dev/null
@@ -1,2 +0,0 @@
-single-debian-patch
-extend-diff-ignore = "^(\.travis\.yml|README.md)$"
diff --git a/debian/tabix.install b/debian/tabix.install
deleted file mode 100644
index 7ef89c7..0000000
--- a/debian/tabix.install
+++ /dev/null
@@ -1,3 +0,0 @@
-bgzip usr/bin
-htsfile usr/bin
-tabix usr/bin
diff --git a/debian/tabix.links b/debian/tabix.links
deleted file mode 100644
index 743712c..0000000
--- a/debian/tabix.links
+++ /dev/null
@@ -1 +0,0 @@
-usr/share/man/man1/tabix.1.gz usr/share/man/man1/bgzip.1.gz
diff --git a/debian/tabix.lintian-overrides b/debian/tabix.lintian-overrides
deleted file mode 100644
index ae52d46..0000000
--- a/debian/tabix.lintian-overrides
+++ /dev/null
@@ -1,3 +0,0 @@
-# False positive
-spelling-error-in-binary usr/bin/bgzip compres compress
-spelling-error-in-binary usr/bin/tabix compres compress
diff --git a/debian/tabix.manpages b/debian/tabix.manpages
deleted file mode 100644
index 751e62f..0000000
--- a/debian/tabix.manpages
+++ /dev/null
@@ -1,2 +0,0 @@
-htsfile.1
-tabix.1
diff --git a/debian/tests/control b/debian/tests/control
deleted file mode 100644
index 1eaf184..0000000
--- a/debian/tests/control
+++ /dev/null
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @, build-essential, @builddeps@
-Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
deleted file mode 100644
index 785e36c..0000000
--- a/debian/tests/run-unit-test
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/bin/bash
-set -e
-
-pkg="htslib"
-
-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
- AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
-fi
-
-cp -aL /usr/share/${pkg}-test/* $AUTOPKGTEST_TMP
-
-cd $AUTOPKGTEST_TMP
-
-sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk
-sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk
-
-make check -j4
-
-echo "PASS"
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index 0354117..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,15 +0,0 @@
-Reference:
- Author: "Heng Li"
- Title: "Tabix: fast retrieval of sequence features from generic TAB-delimited files"
- Journal: Bioinformatics
- Year: 2011
- Volume: 27
- Number: 5
- Pages: 718-719
- DOI: 10.1093/bioinformatics/btq671
- PMID: 21208982
- URL: https://academic.oup.com/bioinformatics/article/27/5/718/262743/Tabix-fast-retrieval-of-sequence-features-from
- eprint: https://academic.oup.com/bioinformatics/article-pdf/27/5/718/5504485/btq671.pdf
-Registry:
- Name: OMICtools
- Entry: OMICS_13459
diff --git a/debian/upstream/tabix.edam b/debian/upstream/tabix.edam
deleted file mode 100644
index 6a11cf6..0000000
--- a/debian/upstream/tabix.edam
+++ /dev/null
@@ -1,16 +0,0 @@
-ontology: EDAM (1.13)
-topic:
- - Sequencing
- - Data management
-scopes:
- - name: summary
- function:
- - Indexing
- inputs:
- - data: Sequence coordinates
- formats: [TSV, BED, GFF]
- - data: Data
- formats: [TSV]
- outputs:
- - data: Data index
- formats: [Tabix index file format]
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 82f61ce..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=4
-opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/htslib-$1.tar.gz/,uversionmangle=s/-rc/~rc/ \
- https://github.com/samtools/htslib/tags .*/v?(\d\S*)\.tar\.gz
--
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