[changes brought forward from 1.2.1-1+rpi1 by Peter Michael Green <plugwash@raspbian.org> at Tue, 29 Sep 2015 19:03:00 +0000]
* Fix bus errors in testsuite.
[changes introduced in 1.2.1-2+rpi1 by Peter Michael Green]
* Cleanup duplicated patching with one version bad that made it impossible to unpack source package
manually.
* Remove single-debian-patch from debian/source/options, it was almost certainly responsible for
the above source package screwup.
[dgit import unpatched htslib 1.3.2-1+rpi1]
--- /dev/null
--- /dev/null
++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
++
--- /dev/null
--- /dev/null
++htslib (1.3.2-1+rpi1) stretch-staging; urgency=medium
++
++ [changes brought forward from 1.2.1-1+rpi1 by Peter Michael Green <plugwash@raspbian.org> at Tue, 29 Sep 2015 19:03:00 +0000]
++ * Fix bus errors in testsuite.
++
++ [changes introduced in 1.2.1-2+rpi1 by Peter Michael Green]
++ * Cleanup duplicated patching with one version bad that made it impossible to unpack source package
++ manually.
++ * Remove single-debian-patch from debian/source/options, it was almost certainly responsible for
++ the above source package screwup.
++
++ -- Raspbian forward porter <root@raspbian.org> Tue, 29 Nov 2016 02:43:40 +0000
++
++htslib (1.3.2-1) unstable; urgency=medium
++
++ * New upstream version
++
++ -- Andreas Tille <tille@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@gmail.com>)
++ Closes: #836190
++ * Add myself to uploaders
++
++ -- Andreas Tille <tille@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@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@Base and fai_read@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@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@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@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@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@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@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@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@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@debian.org> Sat, 16 Nov 2013 15:35:03 +0900
--- /dev/null
--- /dev/null
++9
--- /dev/null
--- /dev/null
++Source: htslib
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++Uploaders: Charles Plessy <plessy@debian.org>,
++ Andreas Tille <tille@debian.org>
++Section: science
++Priority: optional
++Build-Depends: debhelper (>= 9),
++ dh-exec,
++ libcurl4-gnutls-dev,
++ libssl-dev,
++ zlib1g-dev,
++ autoconf
++Standards-Version: 3.9.8
++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: libhts1
++Architecture: any
++Multi-Arch: same
++Section: libs
++Depends: ${shlibs:Depends},
++ ${misc: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: libhts1 (= ${binary:Version}),
++ ${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: htslib-test
++Architecture: all
++Depends: ${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.
--- /dev/null
--- /dev/null
++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@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.
++
--- /dev/null
--- /dev/null
++# 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
--- /dev/null
--- /dev/null
++test/* /usr/share/htslib-test/test
++cram/*.h /usr/share/htslib-test/cram
++cram/*.c /usr/share/htslib-test/cram
++Makefile /usr/share/htslib-test
++*.mk /usr/share/htslib-test
++*.c /usr/share/htslib-test
++*.h /usr/share/htslib-test
--- /dev/null
--- /dev/null
++#! /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/${DEB_HOST_MULTIARCH}/pkgconfig
--- /dev/null
--- /dev/null
++#! /usr/bin/dh-exec
++usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH}
--- /dev/null
--- /dev/null
++# False positive
++libhts1: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libhts.so.* compres compress
--- /dev/null
--- /dev/null
++libhts.so.1 libhts1 #MINVER#
++ _reader_next_line@Base 1.0
++ _regidx_build_index@Base 1.2.1
++#MISSING: 1.3.1# _vcf_parse_format@Base 1.0
++ bam_aux2A@Base 1.0
++ bam_aux2Z@Base 1.0
++ bam_aux2f@Base 1.0
++ bam_aux2i@Base 1.0
++ bam_aux_append@Base 1.0
++ bam_aux_del@Base 1.0
++ bam_aux_get@Base 1.0
++ bam_cigar2qlen@Base 1.0
++ bam_cigar2rlen@Base 1.0
++ bam_construct_seq@Base 1.0
++ bam_copy1@Base 1.0
++ bam_destroy1@Base 1.0
++ bam_dup1@Base 1.0
++ bam_endpos@Base 1.0
++ bam_flag2str@Base 1.0
++ bam_hdr_destroy@Base 1.0
++ bam_hdr_dup@Base 1.0
++ bam_hdr_init@Base 1.0
++ bam_hdr_read@Base 1.0
++ bam_hdr_write@Base 1.0
++ bam_header_to_cram@Base 1.0
++ bam_index_build@Base 1.0
++ bam_init1@Base 1.0
++ bam_mplp_auto@Base 1.0
++ bam_mplp_destroy@Base 1.0
++ bam_mplp_init@Base 1.0
++ bam_mplp_init_overlaps@Base 1.0
++ bam_mplp_set_maxcnt@Base 1.0
++ bam_name2id@Base 1.0
++ bam_plp_auto@Base 1.0
++ bam_plp_destroy@Base 1.0
++ bam_plp_init@Base 1.0
++ bam_plp_init_overlaps@Base 1.0
++ bam_plp_next@Base 1.0
++ bam_plp_push@Base 1.0
++ bam_plp_reset@Base 1.0
++ bam_plp_set_maxcnt@Base 1.0
++ bam_read1@Base 1.0
++ bam_str2flag@Base 1.0
++ bam_write1@Base 1.0
++ bcf_add_filter@Base 1.0
++ bcf_add_id@Base 1.3
++ bcf_calc_ac@Base 1.0
++ bcf_clear@Base 1.0
++ bcf_copy@Base 1.2.1
++ bcf_destroy@Base 1.0
++ bcf_dup@Base 1.0
++ bcf_empty@Base 1.3
++ bcf_enc_vchar@Base 1.0
++ bcf_enc_vfloat@Base 1.0
++ bcf_enc_vint@Base 1.0
++ bcf_float_missing@Base 1.0
++ bcf_float_vector_end@Base 1.0
++ bcf_fmt_array@Base 1.0
++ bcf_fmt_sized_array@Base 1.0
++ bcf_get_fmt@Base 1.0
++ bcf_get_fmt_id@Base 1.1
++ bcf_get_format_string@Base 1.0
++ bcf_get_format_values@Base 1.0
++ bcf_get_info@Base 1.0
++ bcf_get_info_id@Base 1.1
++ bcf_get_info_values@Base 1.0
++ bcf_get_variant_type@Base 1.0
++ bcf_get_variant_types@Base 1.0
++ bcf_gt_type@Base 1.0
++ bcf_has_filter@Base 1.0
++ bcf_hdr_add_hrec@Base 1.0
++ bcf_hdr_add_sample@Base 1.0
++ bcf_hdr_append@Base 1.0
++ bcf_hdr_check_sanity@Base 1.0
++ bcf_hdr_combine@Base 1.0
++ bcf_hdr_destroy@Base 1.0
++ bcf_hdr_dup@Base 1.0
++ bcf_hdr_fmt_text@Base 1.0
++ bcf_hdr_get_hrec@Base 1.0
++ bcf_hdr_get_version@Base 1.0
++ bcf_hdr_id2int@Base 1.0
++ bcf_hdr_init@Base 1.0
++ bcf_hdr_merge@Base 1.3
++ bcf_hdr_parse@Base 1.0
++ bcf_hdr_parse_line@Base 1.0
++ bcf_hdr_parse_sample_line@Base 1.0
++ bcf_hdr_printf@Base 1.0
++ bcf_hdr_read@Base 1.0
++ bcf_hdr_register_hrec@Base 1.0
++ bcf_hdr_remove@Base 1.0
++ bcf_hdr_seqnames@Base 1.0
++ bcf_hdr_set@Base 1.0
++ bcf_hdr_set_samples@Base 1.0
++ bcf_hdr_set_version@Base 1.0
++ bcf_hdr_subset@Base 1.0
++ bcf_hdr_sync@Base 1.0
++ bcf_hdr_write@Base 1.0
++ bcf_header_debug@Base 1.0
++ bcf_hrec_add_key@Base 1.0
++ bcf_hrec_debug@Base 1.0
++ bcf_hrec_destroy@Base 1.0
++ bcf_hrec_dup@Base 1.0
++ bcf_hrec_find_key@Base 1.0
++ bcf_hrec_format@Base 1.0
++ bcf_hrec_set_val@Base 1.0
++ bcf_index@Base 1.0
++ bcf_index_build2@Base 1.3
++ bcf_index_build@Base 1.0
++ bcf_index_load2@Base 1.3
++ bcf_init@Base 1.0
++ bcf_is_snp@Base 1.0
++ bcf_read@Base 1.0
++ bcf_readrec@Base 1.0
++ bcf_remove_allele_set@Base 1.3
++ bcf_remove_alleles@Base 1.0
++ bcf_remove_filter@Base 1.0
++ bcf_sr_add_reader@Base 1.0
++ bcf_sr_destroy@Base 1.0
++ bcf_sr_init@Base 1.0
++ bcf_sr_next_line@Base 1.0
++ bcf_sr_regions_destroy@Base 1.0
++ bcf_sr_regions_flush@Base 1.0
++ bcf_sr_regions_init@Base 1.0
++ bcf_sr_regions_next@Base 1.0
++ bcf_sr_regions_overlap@Base 1.0
++ bcf_sr_regions_seek@Base 1.0
++ bcf_sr_remove_reader@Base 1.0
++ bcf_sr_seek@Base 1.0
++ bcf_sr_set_regions@Base 1.0
++ bcf_sr_set_samples@Base 1.0
++ bcf_sr_set_targets@Base 1.0
++ bcf_sr_strerror@Base 1.2.1
++ bcf_subset@Base 1.0
++ bcf_subset_format@Base 1.0
++ bcf_sweep_bwd@Base 1.0
++ bcf_sweep_destroy@Base 1.0
++ bcf_sweep_fwd@Base 1.0
++ bcf_sweep_hdr@Base 1.0
++ bcf_sweep_init@Base 1.0
++ bcf_translate@Base 1.0
++ bcf_trim_alleles@Base 1.0
++ bcf_type_shift@Base 1.0
++ bcf_unpack@Base 1.0
++ bcf_update_alleles@Base 1.0
++ bcf_update_alleles_str@Base 1.0
++ bcf_update_filter@Base 1.0
++ bcf_update_format@Base 1.0
++ bcf_update_format_string@Base 1.0
++ bcf_update_id@Base 1.0
++ bcf_update_info@Base 1.0
++ bcf_write@Base 1.0
++ bgzf_check_EOF@Base 1.0
++ bgzf_close@Base 1.0
++ bgzf_compress@Base 1.3
++ bgzf_dopen@Base 1.0
++ bgzf_flush@Base 1.0
++ bgzf_flush_try@Base 1.0
++ bgzf_getc@Base 1.0
++ bgzf_getline@Base 1.0
++ bgzf_hopen@Base 1.0
++ bgzf_index_add_block@Base 1.0
++ bgzf_index_build_init@Base 1.0
++ bgzf_index_destroy@Base 1.0
++ bgzf_index_dump@Base 1.0
++ bgzf_index_load@Base 1.0
++ bgzf_is_bgzf@Base 1.0
++ bgzf_mt@Base 1.0
++ bgzf_open@Base 1.0
++ bgzf_raw_read@Base 1.0
++ bgzf_raw_write@Base 1.0
++ bgzf_read@Base 1.0
++ bgzf_read_block@Base 1.0
++ bgzf_seek@Base 1.0
++ bgzf_set_cache_size@Base 1.0
++ bgzf_useek@Base 1.0
++ bgzf_utell@Base 1.0
++ bgzf_write@Base 1.0
++ cram_beta_decode_char@Base 1.0
++ cram_beta_decode_free@Base 1.0
++ cram_beta_decode_init@Base 1.0
++ cram_beta_decode_int@Base 1.0
++ cram_beta_encode_char@Base 1.0
++ cram_beta_encode_free@Base 1.0
++ cram_beta_encode_init@Base 1.0
++ cram_beta_encode_int@Base 1.0
++ cram_beta_encode_store@Base 1.0
++ cram_block_append@Base 1.3
++ cram_block_compression_hdr_decoder2encoder@Base 1.3
++ cram_block_compression_hdr_set_rg@Base 1.3
++ cram_block_get_comp_size@Base 1.3
++ cram_block_get_content_id@Base 1.3
++ cram_block_get_content_type@Base 1.3
++ cram_block_get_crc32@Base 1.3
++ cram_block_get_data@Base 1.3
++ cram_block_get_offset@Base 1.3
++ cram_block_get_size@Base 1.3
++ cram_block_get_uncomp_size@Base 1.3
++ cram_block_method2str@Base 1.0
++ cram_block_set_comp_size@Base 1.3
++ cram_block_set_content_id@Base 1.3
++ cram_block_set_crc32@Base 1.3
++ cram_block_set_data@Base 1.3
++ cram_block_set_offset@Base 1.3
++ cram_block_set_size@Base 1.3
++ cram_block_set_uncomp_size@Base 1.3
++ cram_block_size@Base 1.3
++ cram_block_update_size@Base 1.3
++ cram_byte_array_len_decode@Base 1.0
++ cram_byte_array_len_decode_free@Base 1.0
++ cram_byte_array_len_decode_init@Base 1.0
++ cram_byte_array_len_encode@Base 1.0
++ cram_byte_array_len_encode_free@Base 1.0
++ cram_byte_array_len_encode_init@Base 1.0
++ cram_byte_array_len_encode_store@Base 1.0
++ cram_byte_array_stop_decode_block@Base 1.0
++ cram_byte_array_stop_decode_free@Base 1.0
++ cram_byte_array_stop_decode_init@Base 1.0
++ cram_byte_array_stop_encode@Base 1.0
++ cram_byte_array_stop_encode_free@Base 1.0
++ cram_byte_array_stop_encode_init@Base 1.0
++ cram_byte_array_stop_encode_store@Base 1.0
++ cram_close@Base 1.0
++ cram_codec_decoder2encoder@Base 1.3
++ cram_codec_to_id@Base 1.2.1
++ cram_compress_block@Base 1.0
++ cram_container_get_landmarks@Base 1.3
++ cram_container_get_length@Base 1.3
++ cram_container_get_num_blocks@Base 1.3
++ cram_container_is_empty@Base 1.3
++ cram_container_set_landmarks@Base 1.3
++ cram_container_set_length@Base 1.3
++ cram_container_set_num_blocks@Base 1.3
++ cram_container_size@Base 1.3
++ cram_content_type2str@Base 1.0
++ cram_copy_slice@Base 1.3
++ cram_decode_TD@Base 1.0
++ cram_decode_compression_header@Base 1.0
++ cram_decode_estimate_sizes@Base 1.3
++ cram_decode_slice@Base 1.0
++ cram_decode_slice_header@Base 1.0
++ cram_decode_slice_mt@Base 1.0
++ cram_decode_slice_thread@Base 1.0
++ cram_decoder_init@Base 1.0
++ cram_dependent_data_series@Base 1.2.1
++ cram_dopen@Base 1.0
++ cram_encode_compression_header@Base 1.0
++ cram_encode_container@Base 1.0
++ cram_encode_slice_header@Base 1.0
++ cram_encoder_init@Base 1.0
++ cram_encoding2str@Base 1.0
++ cram_eof@Base 1.0
++ cram_external_decode_char@Base 1.0
++ cram_external_decode_free@Base 1.0
++ cram_external_decode_init@Base 1.0
++ cram_external_decode_int@Base 1.0
++ cram_external_encode_char@Base 1.2.1
++ cram_external_encode_free@Base 1.0
++ cram_external_encode_init@Base 1.0
++ cram_external_encode_int@Base 1.2.1
++ cram_external_encode_store@Base 1.0
++ cram_fd_get_fp@Base 1.3
++ cram_fd_get_header@Base 1.3
++ cram_fd_get_version@Base 1.3
++ cram_fd_set_fp@Base 1.3
++ cram_fd_set_header@Base 1.3
++ cram_fd_set_version@Base 1.3
++ cram_flush@Base 1.0
++ cram_flush_container@Base 1.0
++ cram_flush_container_mt@Base 1.0
++ cram_flush_thread@Base 1.0
++ cram_free_block@Base 1.0
++ cram_free_compression_header@Base 1.0
++ cram_free_container@Base 1.0
++ cram_free_file_def@Base 1.0
++ cram_free_slice@Base 1.0
++ cram_free_slice_header@Base 1.0
++ cram_gamma_decode@Base 1.0
++ cram_gamma_decode_free@Base 1.0
++ cram_gamma_decode_init@Base 1.0
++ cram_get_bam_seq@Base 1.0
++ cram_get_ref@Base 1.0
++ cram_get_seq@Base 1.0
++ cram_header_to_bam@Base 1.0
++ cram_huffman_decode_char0@Base 1.0
++ cram_huffman_decode_char@Base 1.0
++ cram_huffman_decode_free@Base 1.0
++ cram_huffman_decode_init@Base 1.0
++ cram_huffman_decode_int0@Base 1.0
++ cram_huffman_decode_int@Base 1.0
++ cram_huffman_decode_null@Base 1.3
++ cram_huffman_encode_char0@Base 1.0
++ cram_huffman_encode_char@Base 1.0
++ cram_huffman_encode_free@Base 1.0
++ cram_huffman_encode_init@Base 1.0
++ cram_huffman_encode_int0@Base 1.0
++ cram_huffman_encode_int@Base 1.0
++ cram_huffman_encode_store@Base 1.0
++ cram_index_build@Base 1.0
++ cram_index_free@Base 1.0
++ cram_index_load@Base 1.0
++ cram_index_query@Base 1.0
++ cram_load_reference@Base 1.0
++ cram_major_vers@Base 1.3
++ cram_minor_vers@Base 1.3
++ cram_new_block@Base 1.0
++ cram_new_compression_header@Base 1.0
++ cram_new_container@Base 1.0
++ cram_new_metrics@Base 1.0
++ cram_new_slice@Base 1.0
++ cram_open@Base 1.0
++ cram_put_bam_seq@Base 1.0
++ cram_read_SAM_hdr@Base 1.0
++ cram_read_block@Base 1.0
++ cram_read_container@Base 1.0
++ cram_read_file_def@Base 1.0
++ cram_read_slice@Base 1.0
++ cram_ref_decr@Base 1.0
++ cram_ref_incr@Base 1.0
++ cram_ref_load@Base 1.0
++ cram_seek@Base 1.0
++ cram_seek_to_refpos@Base 1.0
++ cram_set_header@Base 1.0
++ cram_set_option@Base 1.0
++ cram_set_voption@Base 1.0
++ cram_slice_hdr_get_num_blocks@Base 1.3
++ cram_stats_add@Base 1.0
++ cram_stats_create@Base 1.0
++ cram_stats_del@Base 1.0
++ cram_stats_dump@Base 1.0
++ cram_stats_encoding@Base 1.0
++ cram_stats_free@Base 1.0
++ cram_store_container@Base 1.3
++ cram_subexp_decode@Base 1.0
++ cram_subexp_decode_free@Base 1.0
++ cram_subexp_decode_init@Base 1.0
++ cram_transcode_rg@Base 1.3
++ cram_uncompress_block@Base 1.0
++ cram_write_SAM_hdr@Base 1.0
++ cram_write_block@Base 1.0
++ cram_write_container@Base 1.0
++ cram_write_file_def@Base 1.0
++ debug_buffer@Base 1.0
++ debug_buffers@Base 1.0
++ expand_cache_path@Base 1.0
++ fai_build@Base 1.0
++ fai_build_core@Base 1.0
++ fai_destroy@Base 1.0
++ fai_fetch@Base 1.0
++ fai_load@Base 1.0
++#MISSING: 1.3.1# fai_read@Base 1.0
++ fai_save@Base 1.0
++ faidx_fetch_nseq@Base 1.2.1
++ faidx_fetch_seq@Base 1.0
++ faidx_has_seq@Base 1.0
++ faidx_iseq@Base 1.1
++ faidx_nseq@Base 1.1
++ faidx_seq_len@Base 1.1
++ file_exists@Base 1.0
++ file_size@Base 1.0
++ find_file_url@Base 1.0
++ find_path@Base 1.3
++ flen@Base 1.0
++ hclose@Base 1.0
++ hclose_abruptly@Base 1.0
++ hdopen@Base 1.0
++ hfile_add_scheme_handler@Base 1.3
++ hfile_always_local@Base 1.3
++ hfile_always_remote@Base 1.3
++ hfile_destroy@Base 1.0
++ hfile_init@Base 1.0
++ hfile_oflags@Base 1.0
++ hfile_plugin_init_libcurl@Base 1.3.1
++ hfile_plugin_init_net@Base 1.3
++ hflush@Base 1.0
++ hgetc2@Base 1.0
++ hisremote@Base 1.2.1
++ hopen@Base 1.0
++ hopen_libcurl@Base 1.3.1
++ hopen_net@Base 1.0
++ hpeek@Base 1.0
++ hputc2@Base 1.0
++ hputs2@Base 1.0
++ hread2@Base 1.0
++ hrec_add_idx@Base 1.0
++ hseek@Base 1.0
++ hts_close@Base 1.0
++ hts_detect_format@Base 1.2.1
++ hts_file_type@Base 1.0
++ hts_format_description@Base 1.2.1
++ hts_format_file_extension@Base 1.3
++ hts_get_bgzfp@Base 1.0
++ hts_get_format@Base 1.2.1
++ hts_getline@Base 1.0
++ hts_hopen@Base 1.2.1
++ hts_idx_destroy@Base 1.0
++ hts_idx_finish@Base 1.0
++ hts_idx_get_meta@Base 1.0
++ hts_idx_get_n_no_coor@Base 1.0
++ hts_idx_get_stat@Base 1.0
++ hts_idx_getfn@Base 1.0
++ hts_idx_init@Base 1.0
++ hts_idx_load2@Base 1.3
++ hts_idx_load@Base 1.0
++ hts_idx_push@Base 1.0
++ hts_idx_save@Base 1.0
++ hts_idx_save_as@Base 1.3
++ hts_idx_seqnames@Base 1.0
++ hts_idx_set_meta@Base 1.0
++ hts_itr_destroy@Base 1.0
++ hts_itr_next@Base 1.0
++ hts_itr_query@Base 1.0
++ hts_itr_querys@Base 1.0
++ hts_md5_destroy@Base 1.3
++ hts_md5_final@Base 1.3
++ hts_md5_hex@Base 1.3
++ hts_md5_init@Base 1.3
++ hts_md5_reset@Base 1.3
++ hts_md5_update@Base 1.3
++ hts_open@Base 1.0
++ hts_open_format@Base 1.3
++ hts_opt_add@Base 1.3
++ hts_opt_apply@Base 1.3
++ hts_opt_free@Base 1.3
++ hts_parse_decimal@Base 1.3
++ hts_parse_format@Base 1.3
++ hts_parse_opt_list@Base 1.3
++ hts_parse_reg@Base 1.0
++ hts_readlines@Base 1.0
++ hts_readlist@Base 1.0
++ hts_set_fai_filename@Base 1.0
++ hts_set_opt@Base 1.2.1
++ hts_set_threads@Base 1.0
++ hts_useek@Base 1.0
++ hts_utell@Base 1.0
++ hts_verbose@Base 1.0
++ hts_version@Base 1.0
++ hwrite2@Base 1.0
++ int32_decode@Base 1.0
++ int32_encode@Base 1.0
++ int32_get_blk@Base 1.3
++ int32_put_blk@Base 1.3
++ is_directory@Base 1.0
++ is_file@Base 1.0
++ itf8_bytes@Base 1.3
++ itf8_decode@Base 1.0
++ itf8_decode_crc@Base 1.3
++ itf8_encode@Base 1.0
++ itf8_put_blk@Base 1.0
++ kf_betai@Base 1.0
++ kf_erfc@Base 1.0
++ kf_gammap@Base 1.0
++ kf_gammaq@Base 1.0
++ kf_lgamma@Base 1.0
++ kftp_connect@Base 1.0
++ kftp_connect_file@Base 1.0
++ kftp_parse_url@Base 1.0
++ kftp_reconnect@Base 1.0
++ kgetline@Base 1.3
++ kh_clear_s2i@Base 1.0
++ kh_del_s2i@Base 1.0
++ kh_destroy_s2i@Base 1.0
++ kh_get_s2i@Base 1.0
++ kh_init_s2i@Base 1.0
++ kh_put_s2i@Base 1.0
++ kh_resize_s2i@Base 1.0
++ khttp_connect_file@Base 1.0
++ khttp_parse_url@Base 1.0
++ kmemmem@Base 1.0
++ knet_close@Base 1.0
++ knet_dopen@Base 1.0
++ knet_open@Base 1.0
++ knet_read@Base 1.0
++ knet_seek@Base 1.0
++ ks_combsort__off@Base 1.0
++ ks_destroy@Base 1.0
++ ks_getuntil2@Base 1.0
++ ks_heapadjust__off@Base 1.0
++ ks_heapmake__off@Base 1.0
++ ks_heapsort__off@Base 1.0
++ ks_init@Base 1.0
++ ks_introsort__off@Base 1.0
++ ks_ksmall__off@Base 1.0
++ ks_mergesort__off@Base 1.0
++ ks_shuffle__off@Base 1.0
++ ksplit_core@Base 1.0
++ ksprintf@Base 1.0
++ kstrnstr@Base 1.0
++ kstrstr@Base 1.0
++ kstrtok@Base 1.0
++ kt_fisher_exact@Base 1.0
++ kvsprintf@Base 1.0
++ ltf8_decode@Base 1.0
++ ltf8_decode_crc@Base 1.3
++ ltf8_get@Base 1.0
++ ltf8_put@Base 1.0
++ mfascii@Base 1.0
++ mfclose@Base 1.0
++ mfcreate@Base 1.0
++ mfcreate_from@Base 1.0
++ mfdestroy@Base 1.0
++ mfdetach@Base 1.0
++ mfeof@Base 1.0
++ mfflush@Base 1.0
++ mfgetc@Base 1.0
++ mfgets@Base 1.0
++ mfmmap@Base 1.3
++ mfopen@Base 1.0
++ mfprintf@Base 1.0
++ mfread@Base 1.0
++ mfrecreate@Base 1.0
++ mfreopen@Base 1.0
++ mfseek@Base 1.0
++ mfsteal@Base 1.0
++ mftell@Base 1.0
++ mftruncate@Base 1.0
++ mfwrite@Base 1.0
++ mkdir_prefix@Base 1.0
++ mrewind@Base 1.0
++ mstderr@Base 1.0
++ mstdin@Base 1.0
++ mstdout@Base 1.0
++ mungetc@Base 1.0
++ open_path_mfile@Base 1.0
++ paranoid_fclose@Base 1.0
++ pool_alloc@Base 1.0
++ pool_create@Base 1.0
++ pool_destroy@Base 1.0
++ pool_free@Base 1.0
++ rans_compress@Base 1.2.1
++ rans_compress_O0@Base 1.2.1
++ rans_compress_O1@Base 1.2.1
++ rans_uncompress@Base 1.2.1
++ rans_uncompress_O0@Base 1.2.1
++ rans_uncompress_O1@Base 1.2.1
++ refs2id@Base 1.0
++ refs_free@Base 1.0
++ regidx_destroy@Base 1.2.1
++ regidx_init@Base 1.2.1
++ regidx_insert@Base 1.2.1
++ regidx_nregs@Base 1.2.1
++ regidx_overlap@Base 1.2.1
++ regidx_parse_bed@Base 1.2.1
++ regidx_parse_tab@Base 1.2.1
++ regidx_seq_names@Base 1.2.1
++ regidx_seq_nregs@Base 1.2.1
++ sam_format1@Base 1.0
++ sam_hdr_PG_ID@Base 1.0
++ sam_hdr_add@Base 1.0
++ sam_hdr_add_PG@Base 1.0
++ sam_hdr_add_lines@Base 1.0
++ sam_hdr_decr_ref@Base 1.0
++ sam_hdr_dump@Base 1.0
++ sam_hdr_dup@Base 1.0
++ sam_hdr_find@Base 1.0
++ sam_hdr_find_key@Base 1.0
++ sam_hdr_find_line@Base 1.0
++ sam_hdr_find_rg@Base 1.0
++ sam_hdr_free@Base 1.0
++ sam_hdr_incr_ref@Base 1.0
++ sam_hdr_length@Base 1.0
++ sam_hdr_link_pg@Base 1.0
++ sam_hdr_name2ref@Base 1.0
++ sam_hdr_new@Base 1.0
++ sam_hdr_parse@Base 1.0
++ sam_hdr_parse_@Base 1.0
++ sam_hdr_read@Base 1.0
++ sam_hdr_rebuild@Base 1.0
++ sam_hdr_sort_order@Base 1.3
++ sam_hdr_str@Base 1.0
++ sam_hdr_update@Base 1.0
++ sam_hdr_vadd@Base 1.0
++ sam_hdr_write@Base 1.0
++ sam_index_build2@Base 1.3
++ sam_index_build@Base 1.3
++ sam_index_load2@Base 1.3
++ sam_index_load@Base 1.0
++ sam_itr_queryi@Base 1.0
++ sam_itr_querys@Base 1.0
++ sam_open_mode@Base 1.0
++ sam_open_mode_opts@Base 1.3
++ sam_parse1@Base 1.0
++ sam_read1@Base 1.0
++ sam_write1@Base 1.0
++ seq_nt16_int@Base 1.2.1
++ seq_nt16_str@Base 1.0
++ seq_nt16_table@Base 1.0
++ string_alloc@Base 1.0
++ string_dup@Base 1.0
++ string_ndup@Base 1.0
++ string_pool_create@Base 1.0
++ string_pool_destroy@Base 1.0
++ stringify_argv@Base 1.0
++ t_pool_delete_result@Base 1.0
++ t_pool_destroy@Base 1.0
++ t_pool_dispatch2@Base 1.0
++ t_pool_dispatch@Base 1.0
++ t_pool_flush@Base 1.0
++ t_pool_init@Base 1.0
++ t_pool_next_result@Base 1.0
++ t_pool_next_result_wait@Base 1.0
++ t_pool_results_queue_empty@Base 1.0
++ t_pool_results_queue_len@Base 1.0
++ t_pool_results_queue_sz@Base 1.0
++ t_results_queue_destroy@Base 1.0
++ t_results_queue_init@Base 1.0
++ tbx_conf_bed@Base 1.0
++ tbx_conf_gff@Base 1.0
++ tbx_conf_psltbl@Base 1.0
++ tbx_conf_sam@Base 1.0
++ tbx_conf_vcf@Base 1.0
++ tbx_destroy@Base 1.0
++ tbx_index@Base 1.0
++ tbx_index_build2@Base 1.3
++ tbx_index_build@Base 1.0
++ tbx_index_load2@Base 1.3
++ tbx_index_load@Base 1.0
++ tbx_name2id@Base 1.0
++ tbx_parse1@Base 1.0
++ tbx_readrec@Base 1.0
++ tbx_seqnames@Base 1.0
++ tbx_set_meta@Base 1.0
++ tokenise_search_path@Base 1.0
++ vcf_format@Base 1.0
++ vcf_hdr_read@Base 1.0
++ vcf_hdr_write@Base 1.0
++ vcf_parse@Base 1.0
++ vcf_read@Base 1.0
++ vcf_write@Base 1.0
++ vcf_write_line@Base 1.0
++ vflen@Base 1.0
++ zfclose@Base 1.0
++ zfeof@Base 1.0
++ zfgets@Base 1.0
++ zfopen@Base 1.0
++ zfpeek@Base 1.0
++ zfputs@Base 1.0
++ zfseeko@Base 1.0
++ zftello@Base 1.0
++ zlib_mem_inflate@Base 1.0
--- /dev/null
--- /dev/null
++Description: Fix alignment issues
++ Fix alignment issues identified through test failure with "BUS error" when
++ building on Debian armhf and raspbian.
++Author: Peter Michael Green <plugwash@raspbian.org>
++
++---
++The information above should follow the Patch Tagging Guidelines, please
++checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
++are templates for supplementary fields that you might want to add:
++
++Origin: <vendor|upstream|other>, <url of original patch>
++Bug: <url in upstream bugtracker>
++Bug-Debian: https://bugs.debian.org/<bugnumber>
++Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
++Forwarded: <no|not-needed|url proving that it has been forwarded>
++Reviewed-By: <name and email of someone who approved the patch>
++Last-Update: <YYYY-MM-DD>
++
++Index: htslib-1.3.1/sam.c
++===================================================================
++--- htslib-1.3.1.orig/sam.c
+++++ htslib-1.3.1/sam.c
++@@ -1069,6 +1069,12 @@ err_recover:
++ }
++ }
++
+++#define READUNALIGNED(ptr,type) ({ \
+++ type tmp;\
+++ memcpy(&tmp,ptr,sizeof(type));\
+++ tmp;\
+++})
+++
++ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
++ {
++ int i;
++@@ -1132,36 +1138,36 @@ int sam_format1(const bam_hdr_t *h, cons
++ } else if (type == 'S') {
++ if (s+2 <= b->data + b->l_data) {
++ kputsn("i:", 2, str);
++- kputw(*(uint16_t*)s, str);
+++ kputw(READUNALIGNED(s,uint16_t), str);
++ s += 2;
++ } else return -1;
++ } else if (type == 's') {
++ if (s+2 <= b->data + b->l_data) {
++ kputsn("i:", 2, str);
++- kputw(*(int16_t*)s, str);
+++ kputw(READUNALIGNED(s,int16_t), str);
++ s += 2;
++ } else return -1;
++ } else if (type == 'I') {
++ if (s+4 <= b->data + b->l_data) {
++ kputsn("i:", 2, str);
++- kputuw(*(uint32_t*)s, str);
+++ kputuw(READUNALIGNED(s,uint32_t), str);
++ s += 4;
++ } else return -1;
++ } else if (type == 'i') {
++ if (s+4 <= b->data + b->l_data) {
++ kputsn("i:", 2, str);
++- kputw(*(int32_t*)s, str);
+++ kputw(READUNALIGNED(s,int32_t), str);
++ s += 4;
++ } else return -1;
++ } else if (type == 'f') {
++ if (s+4 <= b->data + b->l_data) {
++- ksprintf(str, "f:%g", *(float*)s);
+++ ksprintf(str, "f:%g", READUNALIGNED(s,float));
++ s += 4;
++ } else return -1;
++
++ } else if (type == 'd') {
++ if (s+8 <= b->data + b->l_data) {
++- ksprintf(str, "d:%g", *(double*)s);
+++ ksprintf(str, "d:%g", READUNALIGNED(s,double));
++ s += 8;
++ } else return -1;
++ } else if (type == 'Z' || type == 'H') {
++@@ -1185,11 +1191,11 @@ int sam_format1(const bam_hdr_t *h, cons
++ kputc(',', str);
++ if ('c' == sub_type) { kputw(*(int8_t*)s, str); ++s; }
++ else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; }
++- else if ('s' == sub_type) { kputw(*(int16_t*)s, str); s += 2; }
++- else if ('S' == sub_type) { kputw(*(uint16_t*)s, str); s += 2; }
++- else if ('i' == sub_type) { kputw(*(int32_t*)s, str); s += 4; }
++- else if ('I' == sub_type) { kputuw(*(uint32_t*)s, str); s += 4; }
++- else if ('f' == sub_type) { ksprintf(str, "%g", *(float*)s); s += 4; }
+++ else if ('s' == sub_type) { kputw(READUNALIGNED(s,int16_t), str); s += 2; }
+++ else if ('S' == sub_type) { kputw(READUNALIGNED(s,uint16_t), str); s += 2; }
+++ else if ('i' == sub_type) { kputw(READUNALIGNED(s,int32_t), str); s += 4; }
+++ else if ('I' == sub_type) { kputuw(READUNALIGNED(s,uint32_t), str); s += 4; }
+++ else if ('f' == sub_type) { ksprintf(str, "%g", READUNALIGNED(s,float)); s += 4; }
++ else return -1;
++ }
++ }
++@@ -1296,9 +1302,9 @@ int32_t bam_aux2i(const uint8_t *s)
++ type = *s++;
++ if (type == 'c') return (int32_t)*(int8_t*)s;
++ else if (type == 'C') return (int32_t)*(uint8_t*)s;
++- else if (type == 's') return (int32_t)*(int16_t*)s;
++- else if (type == 'S') return (int32_t)*(uint16_t*)s;
++- else if (type == 'i' || type == 'I') return *(int32_t*)s;
+++ else if (type == 's') return (int32_t)READUNALIGNED(s,int16_t);
+++ else if (type == 'S') return (int32_t)READUNALIGNED(s,uint16_t);
+++ else if (type == 'i' || type == 'I') return READUNALIGNED(s,int32_t);
++ else return 0;
++ }
++
++@@ -1306,8 +1312,8 @@ double bam_aux2f(const uint8_t *s)
++ {
++ int type;
++ type = *s++;
++- if (type == 'd') return *(double*)s;
++- else if (type == 'f') return *(float*)s;
+++ if (type == 'd') return READUNALIGNED(s,double);
+++ else if (type == 'f') return READUNALIGNED(s,float);
++ else return 0.0;
++ }
++
--- /dev/null
--- /dev/null
++Author: Andreas Tille <tille@debian.org>,
++ Svante Signell <svante.signell@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
++@@ -153,6 +153,13 @@ extern "C" {
++
++ #endif
++
+++/*
+++ * in case PATH_MAX is not defined (like in hurd)
+++ */
+++#ifndef PATH_MAX
+++# define PATH_MAX 1024
+++#endif
+++
++ /*-----------------------------------------------------------------------------
++ * Allow for unaligned memory access. This is used in BAM code as the packed
++ * structure has 4-byte cigar ints after the variable length name.
++--- a/cram/open_trace_file.c
+++++ b/cram/open_trace_file.c
++@@ -72,9 +72,6 @@ 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"
--- /dev/null
--- /dev/null
++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@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@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)
--- /dev/null
--- /dev/null
++define_PATH_MAX.patch
++literal_version.patch
++alignment.patch
--- /dev/null
--- /dev/null
++#!/usr/bin/make -f
++
++# export DEB_BUILD_MAINT_OPTIONS = hardening=+all # Build fails due to -fpie
++export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
++
++export DH_VERBOSE=1
++DEB_VERSION := $(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ')
++
++%:
++ dh $@ --parallel
++
++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
++ ./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:
++ rm $(CURDIR)/test/sam $(CURDIR)/test/test-regidx
++ dh_auto_install -- \
++ prefix=/usr \
++ libdir=/usr/lib/$(DEB_HOST_MULTIARCH) \
++ PACKAGE_VERSION="$(DEB_VERSION)"
++
++override_dh_installchangelogs:
++ dh_installchangelogs NEWS
--- /dev/null
--- /dev/null
++3.0 (quilt)
--- /dev/null
--- /dev/null
++extend-diff-ignore = "^(\.travis\.yml|README.md)$"
--- /dev/null
--- /dev/null
++tabix usr/bin
++bgzip usr/bin
--- /dev/null
--- /dev/null
++usr/share/man/man1/tabix.1.gz usr/share/man/man1/bgzip.1.gz
--- /dev/null
--- /dev/null
++# False positive
++spelling-error-in-binary usr/bin/bgzip compres compress
++spelling-error-in-binary usr/bin/tabix compres compress
--- /dev/null
--- /dev/null
++tabix.1
--- /dev/null
--- /dev/null
++Tests: run-unit-test
++Depends: @
++Restrictions: allow-stderr
--- /dev/null
--- /dev/null
++#!/bin/bash
++set -e
++
++pkg="htslib"
++
++if [ "$AUTOPKGTEST_TMP" = "" ] ; then
++ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
++fi
++
++cp -a /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"
--- /dev/null
--- /dev/null
++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]
--- /dev/null
--- /dev/null
++version=3
++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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