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.

[dgit import unpatched htslib 1.1-1]

diff --cc debian/changelog
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..df41deedc7d2b4be6c49b07f56cf8b62229a3e89
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/changelog
@@@ -1,0 -1,0 +1,38 @@@
++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

diff --cc debian/compat
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..ec635144f60048986bc560c5576355344005e6e7
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/compat
@@@ -1,0 -1,0 +1,1 @@@
++9

diff --cc debian/control
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..9b8b5ad4fba18ad88f6983a514a9546d8e42998a
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/control
@@@ -1,0 -1,0 +1,61 @@@
++Source: htslib
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++Uploaders: Charles Plessy <plessy@debian.org>
++Section: science
++Priority: optional
++Build-Depends: debhelper (>= 9),
++               dh-exec,
++               zlib1g-dev
++Standards-Version: 3.9.6
++Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/htslib.git
++Vcs-Git: git://anonscm.debian.org/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
++ 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
++ 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 chromosme), 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 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..86ce888e49db3b750ec5c8f084065c5329843326
new file mode 100644 (file)
--- /dev/null
--- /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/1.1.tar.gz
++
++Files: *
++Copyright: © 2012-2014 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: cram/md5.? 
++Copyright: No copyright is claimed
++License: solar-MD5
++ This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
++ MD5 Message-Digest Algorithm (RFC 1321).
++ .
++ Homepage:
++ http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
++ .
++ Author:
++ Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
++ .
++ This software was written by Alexander Peslyak in 2001.  No copyright is
++ claimed, and the software is hereby placed in the public domain.
++ In case this attempt to disclaim copyright and place the software in the
++ public domain is deemed null and void, then the software is
++ Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
++ general public under the following terms:
++ .
++ Redistribution and use in source and binary forms, with or without
++ modification, are permitted.
++ .
++ There's ABSOLUTELY NO WARRANTY, express or implied.
++
++License: MIT
++ Permission is hereby granted, free of charge, to any person obtaining
++ a copy of this software and associated documentation files (the
++ "Software"), to deal in the Software without restriction, including
++ without limitation the rights to use, copy, modify, merge, publish,
++ distribute, sublicense, and/or sell copies of the Software, and to
++ permit persons to whom the Software is furnished to do so, subject to
++ the following conditions:
++ .
++ The above copyright notice and this permission notice shall be
++ included in all copies or substantial portions of the Software.
++ .
++ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
++ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
++ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
++ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
++ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
++ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
++ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
++ SOFTWARE.
++

diff --cc debian/gbp.conf
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..533b17619195f57a31c8b5a17858b855885495a5
new file mode 100644 (file)
--- /dev/null
--- /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 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..c1ef98686448c8acb4aff073bce4edf90eb03113
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/htslib-test.install
@@@ -1,0 -1,0 +1,1 @@@
++test/*        /usr/share/htslib-test

diff --cc debian/libhts-dev.install
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..87e7d23d6074dadafc9d8cf68e86f98b85d699df
new file mode 100755 (executable)
--- /dev/null
--- /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 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..659d59cd1a5d6d20b997eb85d37235cefa0879d8
new file mode 100755 (executable)
--- /dev/null
--- /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.symbols
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..e15b4e305807be4dd15a4bcd4564496e8f71ecfc
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/libhts1.symbols
@@@ -1,0 -1,0 +1,534 @@@
++libhts.so.1 libhts1 #MINVER#
++ MD5_Final@Base 1.0
++ MD5_Init@Base 1.0
++ MD5_Update@Base 1.0
++ _reader_next_line@Base 1.0
++ _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_calc_ac@Base 1.0
++ bcf_clear@Base 1.0
++ bcf_destroy@Base 1.0
++ bcf_dup@Base 1.0
++ bcf_empty1@Base 1.0
++ 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_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_build@Base 1.0
++ bcf_init@Base 1.0
++ bcf_is_snp@Base 1.0
++ bcf_read@Base 1.0
++ bcf_readrec@Base 1.0
++ 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_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_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_method2str@Base 1.0
++ 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_char@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_compress_block@Base 1.0
++ cram_content_type2str@Base 1.0
++ cram_decode_TD@Base 1.0
++ cram_decode_compression_header@Base 1.0
++ 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_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_block@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@Base 1.0
++ cram_external_encode_free@Base 1.0
++ cram_external_encode_init@Base 1.0
++ cram_external_encode_store@Base 1.0
++ 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_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_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_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_subexp_decode@Base 1.0
++ cram_subexp_decode_free@Base 1.0
++ cram_subexp_decode_init@Base 1.0
++ 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
++ download_and_open@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
++ fai_read@Base 1.0
++ fai_save@Base 1.0
++#MISSING: 1.1# faidx_fetch_nseq@Base 1.0
++ 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
++ flen@Base 1.0
++ hclose@Base 1.0
++ hclose_abruptly@Base 1.0
++ hdopen@Base 1.0
++ hfile_destroy@Base 1.0
++ hfile_init@Base 1.0
++ hfile_oflags@Base 1.0
++ hflush@Base 1.0
++ hgetc2@Base 1.0
++ hopen@Base 1.0
++ 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_file_type@Base 1.0
++ hts_get_bgzfp@Base 1.0
++ hts_getline@Base 1.0
++ 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_load@Base 1.0
++ hts_idx_load_local@Base 1.0
++ hts_idx_push@Base 1.0
++ hts_idx_save@Base 1.0
++ 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_open@Base 1.0
++ 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_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@Base 1.0
++ int32_put@Base 1.0
++ is_directory@Base 1.0
++ is_file@Base 1.0
++ itf8_decode@Base 1.0
++ 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
++ 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_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
++ 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
++ refs2id@Base 1.0
++ refs_free@Base 1.0
++ 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_str@Base 1.0
++ sam_hdr_update@Base 1.0
++ sam_hdr_vadd@Base 1.0
++ sam_hdr_write@Base 1.0
++ 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_parse1@Base 1.0
++ sam_read1@Base 1.0
++ sam_write1@Base 1.0
++ 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_build@Base 1.0
++ 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/debian-changes
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..5042628778e07c31665e3b93fca67033bd14f5fc
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/patches/debian-changes
@@@ -1,0 -1,0 +1,61 @@@
++Description: <short summary of the patch>
++ TODO: Put a short summary on the line above and replace this paragraph
++ with a longer explanation of this change. Complete the meta-information
++ with other relevant fields (see below for details). To make it easier, the
++ information below has been extracted from the changelog. Adjust it or drop
++ it.
++ .
++ 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.
++Author: Charles Plessy <plessy@debian.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>
++
++--- /dev/null
+++++ htslib-1.1/.travis.yml
++@@ -0,0 +1,8 @@
+++# Control file for continuous integration testing at http://travis-ci.org/
+++
+++language: c
+++compiler:
+++  - clang
+++  - gcc
+++
+++script: make -e && make test
++--- /dev/null
+++++ htslib-1.1/README.md
++@@ -0,0 +1,17 @@
+++HTSlib is an implementation of a unified C library for accessing common file
+++formats, such as [SAM, CRAM and VCF][1], used for high-throughput sequencing
+++data, and is the core library used by [samtools][2] and [bcftools][3].
+++HTSlib only depends on [zlib][4].
+++It is known to be compatible with gcc, g++ and clang.
+++
+++HTSlib implements a generalized BAM 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 project also includes the popular tabix indexer, which indexes both `.tbi`
+++and `.csi` formats, and the bgzip compression utility.
+++
+++[1]: http://samtools.github.io/hts-specs/
+++[2]: http://github.com/samtools/samtools
+++[3]: http://samtools.github.io/bcftools/
+++[4]: http://zlib.net/

diff --cc debian/patches/series
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..7bb825291d58299d9de235ed4046a594e6a3e035
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/patches/series
@@@ -1,0 -1,0 +1,1 @@@
++debian-changes

diff --cc debian/rules
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..354eafbddf38b085439b33b50a420e43d8980ab2
new file mode 100755 (executable)
--- /dev/null
--- /dev/null
+++ b/debian/rules
@@@ -1,0 -1,0 +1,28 @@@
++#!/usr/bin/make -f
++
++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_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 $(CURDIR)/test/sam
++      dh_auto_install -- \
++        prefix=/usr \
++        libdir=/usr/lib/$(DEB_HOST_MULTIARCH) \
++        PACKAGE_VERSION="$(DEB_VERSION)"

diff --cc debian/source/format
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..163aaf8d82b6c54f23c45f32895dbdfdcc27b047
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/source/format
@@@ -1,0 -1,0 +1,1 @@@
++3.0 (quilt)

diff --cc debian/source/options
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..7423a2df3dbfe7b87c8f4ccb7de206b49dc9d66e
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/source/options
@@@ -1,0 -1,0 +1,1 @@@
++single-debian-patch

diff --cc debian/tabix.install
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..431c7348ae3c85c8666aba7327124c93ae1d8a7c
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/tabix.install
@@@ -1,0 -1,0 +1,2 @@@
++tabix usr/bin
++bgzip usr/bin

diff --cc debian/tabix.links
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..743712c3931d127ad64a09cedecbdf0841e23dd7
new file mode 100644 (file)
--- /dev/null
--- /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.manpages
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..bb616e01fbd33fc9954ec1330293632b6011f320
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/tabix.manpages
@@@ -1,0 -1,0 +1,1 @@@
++tabix.1

diff --cc debian/watch
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..328a1d934c73afc05d8f320f902c190871e0c4ad
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/watch
@@@ -1,0 -1,0 +1,3 @@@
++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