From: Andreas Tille Date: Sat, 14 Jan 2017 18:23:52 +0000 (+0000) Subject: htslib (1.3.2-2) unstable; urgency=medium X-Git-Tag: archive/raspbian/1.3.2-2+rpi1^2~3 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=f66f41429f1c070bbe6a27171d93d9b34c446ab3;p=htslib.git htslib (1.3.2-2) unstable; urgency=medium * Add build-essential and @builddeps@ to autopkgtest * debhelper 10 * d/watch: version=4 [dgit import unpatched htslib 1.3.2-2] --- f66f41429f1c070bbe6a27171d93d9b34c446ab3 diff --cc debian/README.source index 0000000,0000000..4d5e090 new file mode 100644 --- /dev/null +++ b/debian/README.source @@@ -1,0 -1,0 +1,37 @@@ ++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 ++ ++ 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_.orig.tar.gz ++ ++ 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 --cc debian/changelog index 0000000,0000000..f77e67a new file mode 100644 --- /dev/null +++ b/debian/changelog @@@ -1,0 -1,0 +1,126 @@@ ++htslib (1.3.2-2) unstable; urgency=medium ++ ++ * Add build-essential and @builddeps@ to autopkgtest ++ * debhelper 10 ++ * d/watch: version=4 ++ ++ -- Andreas Tille Sat, 14 Jan 2017 19:23:52 +0100 ++ ++htslib (1.3.2-1) unstable; urgency=medium ++ ++ * New upstream version ++ ++ -- Andreas Tille 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 ++ ) ++ Closes: #836190 ++ * Add myself to uploaders ++ ++ -- Andreas Tille 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 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 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 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 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 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 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 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 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 Sun, 17 Aug 2014 20:12:28 +0900 ++ ++htslib (0.2.0~rc3-1) unstable; urgency=low ++ ++ * Initial release. (Closes: #729282) ++ ++ -- Charles Plessy Sat, 16 Nov 2013 15:35:03 +0900 diff --cc debian/compat index 0000000,0000000..f599e28 new file mode 100644 --- /dev/null +++ b/debian/compat @@@ -1,0 -1,0 +1,1 @@@ ++10 diff --cc debian/control index 0000000,0000000..ac24e91 new file mode 100644 --- /dev/null +++ b/debian/control @@@ -1,0 -1,0 +1,85 @@@ ++Source: htslib ++Maintainer: Debian Med Packaging Team ++Uploaders: Charles Plessy , ++ Andreas Tille ++Section: science ++Priority: optional ++Build-Depends: debhelper (>= 10), ++ 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. diff --cc debian/copyright index 0000000,0000000..a923ec3 new file mode 100644 --- /dev/null +++ b/debian/copyright @@@ -1,0 -1,0 +1,117 @@@ ++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 ++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 ++ . ++ 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 --cc debian/gbp.conf index 0000000,0000000..533b176 new file mode 100644 --- /dev/null +++ b/debian/gbp.conf @@@ -1,0 -1,0 +1,15 @@@ ++# 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 --cc debian/htslib-test.install index 0000000,0000000..a9d8290 new file mode 100644 --- /dev/null +++ b/debian/htslib-test.install @@@ -1,0 -1,0 +1,7 @@@ ++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 diff --cc debian/libhts-dev.install index 0000000,0000000..87e7d23 new file mode 100755 --- /dev/null +++ b/debian/libhts-dev.install @@@ -1,0 -1,0 +1,6 @@@ ++#! /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/${DEB_HOST_MULTIARCH}/pkgconfig diff --cc debian/libhts1.install index 0000000,0000000..659d59c new file mode 100755 --- /dev/null +++ b/debian/libhts1.install @@@ -1,0 -1,0 +1,2 @@@ ++#! /usr/bin/dh-exec ++usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH} diff --cc debian/libhts1.lintian-overrides index 0000000,0000000..e53f49f new file mode 100644 --- /dev/null +++ b/debian/libhts1.lintian-overrides @@@ -1,0 -1,0 +1,2 @@@ ++# False positive ++libhts1: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libhts.so.* compres compress diff --cc debian/libhts1.symbols index 0000000,0000000..15a90ae new file mode 100644 --- /dev/null +++ b/debian/libhts1.symbols @@@ -1,0 -1,0 +1,639 @@@ ++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 diff --cc debian/patches/define_PATH_MAX.patch index 0000000,0000000..5bfd09a new file mode 100644 --- /dev/null +++ b/debian/patches/define_PATH_MAX.patch @@@ -1,0 -1,0 +1,37 @@@ ++Author: Andreas Tille , ++ Svante Signell ++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 ++ #include ++ #include "cram/os.h" ++-#ifndef PATH_MAX ++-# define PATH_MAX 1024 ++-#endif ++ ++ #include "cram/open_trace_file.h" ++ #include "cram/misc.h" diff --cc debian/patches/literal_version.patch index 0000000,0000000..be9c8e2 new file mode 100644 --- /dev/null +++ b/debian/patches/literal_version.patch @@@ -1,0 -1,0 +1,16 @@@ ++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 ++--- 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) diff --cc debian/patches/series index 0000000,0000000..3c1f11a new file mode 100644 --- /dev/null +++ b/debian/patches/series @@@ -1,0 -1,0 +1,2 @@@ ++define_PATH_MAX.patch ++literal_version.patch diff --cc debian/rules index 0000000,0000000..1f01d43 new file mode 100755 --- /dev/null +++ b/debian/rules @@@ -1,0 -1,0 +1,38 @@@ ++#!/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 $@ ++ ++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="$(DEB_VERSION)" ++ ++override_dh_installchangelogs: ++ dh_installchangelogs NEWS diff --cc debian/source/format index 0000000,0000000..163aaf8 new file mode 100644 --- /dev/null +++ b/debian/source/format @@@ -1,0 -1,0 +1,1 @@@ ++3.0 (quilt) diff --cc debian/source/options index 0000000,0000000..9511377 new file mode 100644 --- /dev/null +++ b/debian/source/options @@@ -1,0 -1,0 +1,2 @@@ ++single-debian-patch ++extend-diff-ignore = "^(\.travis\.yml|README.md)$" diff --cc debian/tabix.install index 0000000,0000000..431c734 new file mode 100644 --- /dev/null +++ b/debian/tabix.install @@@ -1,0 -1,0 +1,2 @@@ ++tabix usr/bin ++bgzip usr/bin diff --cc debian/tabix.links index 0000000,0000000..743712c new file mode 100644 --- /dev/null +++ b/debian/tabix.links @@@ -1,0 -1,0 +1,1 @@@ ++usr/share/man/man1/tabix.1.gz usr/share/man/man1/bgzip.1.gz diff --cc debian/tabix.lintian-overrides index 0000000,0000000..ae52d46 new file mode 100644 --- /dev/null +++ b/debian/tabix.lintian-overrides @@@ -1,0 -1,0 +1,3 @@@ ++# False positive ++spelling-error-in-binary usr/bin/bgzip compres compress ++spelling-error-in-binary usr/bin/tabix compres compress diff --cc debian/tabix.manpages index 0000000,0000000..bb616e0 new file mode 100644 --- /dev/null +++ b/debian/tabix.manpages @@@ -1,0 -1,0 +1,1 @@@ ++tabix.1 diff --cc debian/tests/control index 0000000,0000000..1eaf184 new file mode 100644 --- /dev/null +++ b/debian/tests/control @@@ -1,0 -1,0 +1,3 @@@ ++Tests: run-unit-test ++Depends: @, build-essential, @builddeps@ ++Restrictions: allow-stderr diff --cc debian/tests/run-unit-test index 0000000,0000000..314636e new file mode 100644 --- /dev/null +++ b/debian/tests/run-unit-test @@@ -1,0 -1,0 +1,19 @@@ ++#!/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" diff --cc debian/upstream/tabix.edam index 0000000,0000000..6a11cf6 new file mode 100644 --- /dev/null +++ b/debian/upstream/tabix.edam @@@ -1,0 -1,0 +1,16 @@@ ++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 --cc debian/watch index 0000000,0000000..82f61ce new file mode 100644 --- /dev/null +++ b/debian/watch @@@ -1,0 -1,0 +1,3 @@@ ++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