From: Charles Plessy Date: Wed, 24 Sep 2014 12:24:11 +0000 (+0000) Subject: Import htslib_1.1-1.debian.tar.xz X-Git-Tag: archive/raspbian/1.3.2-2+rpi1~1^2^2^2~1^2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=6a79fb76f17c18a0e80563942121235347a27a14;p=htslib.git Import htslib_1.1-1.debian.tar.xz [dgit import tarball htslib 1.1-1 htslib_1.1-1.debian.tar.xz] --- 6a79fb76f17c18a0e80563942121235347a27a14 diff --git a/changelog b/changelog new file mode 100644 index 0000000..df41dee --- /dev/null +++ b/changelog @@ -0,0 +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 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 --git a/compat b/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +9 diff --git a/control b/control new file mode 100644 index 0000000..9b8b5ad --- /dev/null +++ b/control @@ -0,0 +1,61 @@ +Source: htslib +Maintainer: Debian Med Packaging Team +Uploaders: Charles Plessy +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 --git a/copyright b/copyright new file mode 100644 index 0000000..86ce888 --- /dev/null +++ b/copyright @@ -0,0 +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 +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 + . + This software was written by Alexander Peslyak in 2001. No copyright is + claimed, and the software is hereby placed in the public domain. + In case this attempt to disclaim copyright and place the software in the + public domain is deemed null and void, then the software is + Copyright (c) 2001 Alexander Peslyak and it is hereby released to the + general public under the following terms: + . + Redistribution and use in source and binary forms, with or without + modification, are permitted. + . + There's ABSOLUTELY NO WARRANTY, express or implied. + +License: MIT + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + . + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + diff --git a/gbp.conf b/gbp.conf new file mode 100644 index 0000000..533b176 --- /dev/null +++ b/gbp.conf @@ -0,0 +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 --git a/htslib-test.install b/htslib-test.install new file mode 100644 index 0000000..c1ef986 --- /dev/null +++ b/htslib-test.install @@ -0,0 +1 @@ +test/* /usr/share/htslib-test diff --git a/libhts-dev.install b/libhts-dev.install new file mode 100755 index 0000000..87e7d23 --- /dev/null +++ b/libhts-dev.install @@ -0,0 +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/${DEB_HOST_MULTIARCH}/pkgconfig diff --git a/libhts1.install b/libhts1.install new file mode 100755 index 0000000..659d59c --- /dev/null +++ b/libhts1.install @@ -0,0 +1,2 @@ +#! /usr/bin/dh-exec +usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH} diff --git a/libhts1.symbols b/libhts1.symbols new file mode 100644 index 0000000..e15b4e3 --- /dev/null +++ b/libhts1.symbols @@ -0,0 +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 --git a/patches/debian-changes b/patches/debian-changes new file mode 100644 index 0000000..5042628 --- /dev/null +++ b/patches/debian-changes @@ -0,0 +1,61 @@ +Description: + 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 + +--- +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: , +Bug: +Bug-Debian: https://bugs.debian.org/ +Bug-Ubuntu: https://launchpad.net/bugs/ +Forwarded: +Reviewed-By: +Last-Update: + +--- /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 --git a/patches/series b/patches/series new file mode 100644 index 0000000..7bb8252 --- /dev/null +++ b/patches/series @@ -0,0 +1 @@ +debian-changes diff --git a/rules b/rules new file mode 100755 index 0000000..354eafb --- /dev/null +++ b/rules @@ -0,0 +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 --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/source/options b/source/options new file mode 100644 index 0000000..7423a2d --- /dev/null +++ b/source/options @@ -0,0 +1 @@ +single-debian-patch diff --git a/tabix.install b/tabix.install new file mode 100644 index 0000000..431c734 --- /dev/null +++ b/tabix.install @@ -0,0 +1,2 @@ +tabix usr/bin +bgzip usr/bin diff --git a/tabix.links b/tabix.links new file mode 100644 index 0000000..743712c --- /dev/null +++ b/tabix.links @@ -0,0 +1 @@ +usr/share/man/man1/tabix.1.gz usr/share/man/man1/bgzip.1.gz diff --git a/tabix.manpages b/tabix.manpages new file mode 100644 index 0000000..bb616e0 --- /dev/null +++ b/tabix.manpages @@ -0,0 +1 @@ +tabix.1 diff --git a/watch b/watch new file mode 100644 index 0000000..328a1d9 --- /dev/null +++ b/watch @@ -0,0 +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