--- /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
+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
+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
+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
+# 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
+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
+#! /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/${DEB_HOST_MULTIARCH}/pkgconfig
--- /dev/null
+#! /usr/bin/dh-exec
+usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH}
--- /dev/null
+# False positive
+libhts1: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libhts.so.* compres compress
--- /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
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+ cram_block_get_crc32@Base 1.3
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+ 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
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+ cram_byte_array_stop_decode_block@Base 1.0
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+ cram_byte_array_stop_encode@Base 1.0
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+ 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
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+ cram_gamma_decode@Base 1.0
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+ 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
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+ 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
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+ cram_major_vers@Base 1.3
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+ cram_new_metrics@Base 1.0
+ cram_new_slice@Base 1.0
+ cram_open@Base 1.0
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+ cram_read_block@Base 1.0
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+ cram_read_file_def@Base 1.0
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+ cram_set_option@Base 1.0
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+ 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
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+ 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
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+ 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
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+ 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
+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
+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
+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
+define_PATH_MAX.patch
+literal_version.patch
+alignment.patch
--- /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="$(DEB_VERSION)"
+
+override_dh_installchangelogs:
+ dh_installchangelogs NEWS
--- /dev/null
+3.0 (quilt)
--- /dev/null
+extend-diff-ignore = "^(\.travis\.yml|README.md)$"
--- /dev/null
+tabix usr/bin
+bgzip usr/bin
--- /dev/null
+usr/share/man/man1/tabix.1.gz usr/share/man/man1/bgzip.1.gz
--- /dev/null
+# False positive
+spelling-error-in-binary usr/bin/bgzip compres compress
+spelling-error-in-binary usr/bin/tabix compres compress
--- /dev/null
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
--- /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
+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
+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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