Git log: commit 765419270800864fd29cea90db233a60cd46aea8
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 16:36:14 2017 +0200
install htslib*.mk files that are used in bcftools
commit 3ccc8bd1c8512d4c6658b7da86276f856a8847ca
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 13:08:44 2017 +0200
hardening=+all
commit bee0b75b05f714072610212975225d233338351f
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 08:09:26 2017 +0200
Refresh patches
commit e335d9b3e2a08a6b5a0331b5106ac348af6652fc
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 08:08:53 2017 +0200
do not parse d/changelog explicitly
commit d3b4f02ce5c1166a5f9514a7c93e92a863b67930
Author: Andreas Tille <tille@debian.org>
Date: Thu Jul 20 08:06:50 2017 +0200
Standards-Version: 4.0.0 (no changes needed)
commit 8ce1126f0fd7d4c8655f9c779440d56c91a1447c
Merge: 78d31d7 ada885d
Author: Steffen Moeller <moeller@debian.org>
Date: Thu Jul 20 12:41:54 2017 +0200
Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable
commit 78d31d74b46caa950a6d480efb5a3ce49993bf1a
Author: Steffen Moeller <moeller@debian.org>
Date: Thu Jul 20 12:40:02 2017 +0200
Added ref to OMICtools
commit ada885d3985096b9b32b19f087f5db1134f07cfd
Author: Andreas Tille <tille@debian.org>
Date: Wed Jul 19 21:53:58 2017 +0200
New upstream version
commit ffd8e1101c57a95a87239189c5cb12652a890c71
Merge: 7b16102 49fdfbd
Author: Andreas Tille <tille@debian.org>
Date: Wed Jul 19 21:52:19 2017 +0200
Merge tag '1.5' into debian/unstable
Noteworthy changes in release 1.5 (21st June 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Added a new logging API: hts_log(), along with hts_log_error(),
hts_log_warn() etc. convenience macros. Thanks go to Anders Kaplan
for the implementation. (#499, #543, #551)
* Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to
alter the hFILE buffer size.
* Fixed various bugs, including compilation issues samtools/bcftools#610,
samtools/bcftools#611 and robustness to corrupted data #537, #538,
#541, #546, #548, #549, #554.
commit 7b16102386e39e76af0fa1609fc4f2e34e8a5654
Author: Graham Inggs <ginggs@debian.org>
Date: Wed Jul 19 10:40:28 2017 +0200
Dereference symlinks to fix autopkgtest
commit 942393ba9a43828c3963dbde066b001dfe96440c
Author: Graham Inggs <ginggs@debian.org>
Date: Tue Jul 18 00:54:22 2017 +0200
Fix FTBFS on s390x and sparc64
commit 485cda1a9936c7edcc890c6b6dc3a76a90cd1f7b
Author: Sascha Steinbiss <satta@debian.org>
Date: Mon Jul 17 18:54:57 2017 +0200
fix FTBFS
commit b8c5413335d426e886068b34c0403639c03bb9dc
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 14:19:42 2017 +0200
Upload to unstable
commit ab6cc2a1149dd695376880ef84da8dcd1c06fbcc
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 14:19:15 2017 +0200
Create symlinks only for arch=indep target when target dir exists
commit 04bb939d7306281768a0f42c6e0da2c00ed79893
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 00:21:02 2017 +0200
Upload to unstable
commit 68e8b5706f4ca4420921ef5b1a3a4b3fa11fea59
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 00:16:58 2017 +0200
New upstream version
commit e8b1b66a95bc6972b8abb7b14688ee0b618b3e4a
Merge: d6cab91 6c06833
Author: Andreas Tille <tille@debian.org>
Date: Sun Jun 18 00:10:48 2017 +0200
Merge tag '1.4.1' into debian/unstable
Noteworthy changes in release 1.4.1 (8th May 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is primarily a security bug fix update.
* Fixed SECURITY issue with buffer overruns with malicious data. (#514).
* S3 support for non Amazon AWS endpoints. (#506)
* Support for variant breakpoints in bcftools. (#516)
* Improved handling of BCF NaNs. (#485)
* Compilation / portability improvements. (#255, #423, #498, #488)
* Miscellaneous bug fixes (#482, #521, #522, #523, #524).
* Sanitise headers (#509)
commit d6cab913f23c6557b430fa9a2e02a5af9f3f94a7
Author: Andreas Tille <tille@debian.org>
Date: Thu May 4 10:57:51 2017 +0200
add the cram_to_bam function to the public interface of htslib because it is used by code in Sambamba
commit 903f2b3b60d716cb65a764970232e0596d45ec01
Author: Andreas Tille <tille@debian.org>
Date: Tue May 2 15:42:35 2017 +0200
Upload to experimental
commit 02e2be3c316268deff361f5bf2a8fbbd37623a2e
Author: Andreas Tille <tille@debian.org>
Date: Tue May 2 15:40:42 2017 +0200
Include htsfile binary into tabix package since its used by manta package
commit d6ae67daffa4819cfc0a913d6a6fbab338f82f8a
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 21:30:16 2017 +0100
hange library name to match soname
commit f711b01663ee28387dd1c704f4cccd9854f03764
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 21:22:09 2017 +0100
Remove symbols file since I'm too lazy to maintain these - volunteers welcome for a final upload to instable
commit 28af9f8c0129302a9f7843d341da3ace2afa7662
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 21:21:20 2017 +0100
Remove binary files from test results
commit 46d5eee361c2c79d9b941d0ab0a154171b4d8d67
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 19:03:50 2017 +0100
Drop autoconf from Build-Depends, add libbz2-dev and liblzma-dev to Build-Depends
commit e742362d5a953ceda3b6d329ce2f3c3a2cbe1219
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 17:43:53 2017 +0100
Update patches
commit 94d9711102d247c6764f216dbebc13795557397a
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 17:42:12 2017 +0100
New upstream version
commit 0172fe3e7ff918bd2c1d594893b2aa76b0b3aca9
Merge: 54feaaa d2d9c76
Author: Andreas Tille <tille@debian.org>
Date: Tue Mar 21 17:40:46 2017 +0100
Merge tag '1.4' into debian/unstable
Relase 1.4 (13 March 2017)
* Incompatible changes: several functions and data types have been changed
in this release, and the shared library soversion has been bumped to 2.
- bam_pileup1_t has an additional field (which holds user data)
- bam1_core_t has been modified to allow for >64K CIGAR operations
and (along with bam1_t) so that CIGAR entries are aligned in memory
- hopen() has vararg arguments for setting URL scheme-dependent options
- the various tbx_conf_* presets are now const
- auxiliary fields in bam1_t are now always stored in little-endian byte
order (previously this depended on if you read a bam, sam or cram file)
- index metadata (accessible via hts_idx_get_meta()) is now always
stored in little-endian byte order (previously this depended on if
the index was in tbi or csi format)
- bam_aux2i() now returns an int64_t value
- fai_load() will no longer save local copies of remote fasta indexes
- hts_idx_get_meta() now takes a uint32_t * for l_meta (was int32_t *)
* HTSlib now links against libbz2 and liblzma by default. To remove these
dependencies, run configure with options --disable-bz2 and --disable-lzma,
but note that this may make some CRAM files produced elsewhere unreadable.
* Added a thread pool interface and replaced the bgzf multi-threading
code to use this pool. BAM and CRAM decoding is now multi-threaded
too, using the pool to automatically balance the number of threads
between decode, encode and any data processing jobs.
* New errmod_cal(), probaln_glocal(), sam_cap_mapq(), and sam_prob_realn()
functions, previously internal to SAMtools, have been added to HTSlib.
* Files can now be accessed via Google Cloud Storage using gs: URLs, when
HTSlib is configured to use libcurl for network file access rather than
the included basic knetfile networking.
* S3 file access now also supports the "host_base" setting in the
$HOME/.s3cfg configuration file.
* Data URLs ("data:,text") now follow the standard RFC 2397 format and may
be base64-encoded (when written as "data:;base64,text") or may include
percent-encoded characters. HTSlib's previous over-simplified "data:text"
format is no longer supported -- you will need to add an initial comma.
* When plugins are enabled, S3 support is now provided by a separate
hfile_s3 plugin rather than by hfile_libcurl itself as previously.
When --enable-libcurl is used, by default both GCS and S3 support
and plugins will also be built; they can be individually disabled
via --disable-gcs and --disable-s3.
* The iRODS file access plugin has been moved to a separate repository.
Configure no longer has a --with-irods option; instead build the plugin
found at <https://github.com/samtools/htslib-plugins>.
* APIs to portably read and write (possibly unaligned) data in little-endian
byte order have been added.
* New functions bam_auxB_len(), bam_auxB2i() and bam_auxB2f() have been
added to make accessing array-type auxiliary data easier. bam_aux2i()
can now return the full range of values that can be stored in an integer
tag (including unsigned 32 bit tags). bam_aux2f() will return the value
of integer tags (as a double) as well as floating-point ones. All of
the bam_aux2 and bam_auxB2 functions will set errno if the requested
conversion is not valid.
* New functions fai_load3() and fai_build3() allow fasta indexes to be
stored in a different location to the indexed fasta file.
* New functions bgzf_index_dump_hfile() and bgzf_index_load_hfile()
allow bgzf index files (.gzi) to be written to / read from an existing
hFILE handle.
* hts_idx_push() will report when trying to add a range to an index that
is beyond the limits that the given index can handle. This means trying
to index chromosomes longer than 2^29 bases with a .bai or .tbi index
will report an error instead of apparantly working but creating an invalid
index entry.
* VCF formatting is now approximately 4x faster. (Whether this is
noticable depends on what was creating the VCF.)
* CRAM lossy_names mode now works with TLEN of 0 or TLEN within +/- 1
of the computed value. Note in these situations TLEN will be
generated / fixed during CRAM decode.
* CRAM now supports bzip2 and lzma codecs. Within htslib these are
disabled by default, but can be enabled by specifying "use_bzip2" or
"use_lzma" in an hts_opt_add() call or via the mode string of the
hts_open_format() function.
commit 54feaaa247be6e99fa472bc9fc8b471848cc5568
Author: Andreas Tille <tille@debian.org>
Date: Fri Feb 10 08:46:42 2017 +0100
Upload to experimental
commit e4ea80c3c5f3f2992033ca62166dd2ee132883ab
Author: Andreas Tille <tille@debian.org>
Date: Thu Feb 9 15:22:18 2017 +0100
Fix pkg-config
commit 44f77d577ac0b4c15f80606274142b388ec8c0d0
Author: Andreas Tille <tille@debian.org>
Date: Thu Feb 9 14:30:46 2017 +0100
Install header files from cram dir in -dev package since these are used in libseqlib
commit 536682b04feffea28b9073db4f0b29d2bc4f3d46
Merge: cf5950e 1b39d8d
Author: Steffen Moeller <moeller@debian.org>
Date: Mon Jan 23 00:46:04 2017 +0100
Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable
commit cf5950e6665f99ebd1b477a635d26282ead4acc9
Author: Steffen Moeller <moeller@debian.org>
Date: Mon Jan 23 00:44:34 2017 +0100
Added reference to tabix
There is none for the HTSlib source package. Maybe one should also
add a reference for SAMtools.
commit 1b39d8d35c5ce1126b12d66e11280fa83d7bd8e4
Author: Andreas Tille <tille@debian.org>
Date: Sat Jan 14 22:11:18 2017 +0100
Add @builddeps@ to autopkgtest
commit f24104ed6b2c22b139fdadb58abb9788cd2d0f41
Author: Andreas Tille <tille@debian.org>
Date: Sat Jan 14 19:23:48 2017 +0100
d/watch: version=4
commit e9945fc7c56a4cd1c6cfb0a2ccf1de0aa848f25d
Author: Andreas Tille <tille@debian.org>
Date: Sat Jan 14 19:22:23 2017 +0100
debhelper 10
commit 6fb42cf5ed95af7b5e3c1ba9c1479bc94b2cde7d
Author: Andreas Tille <tille@debian.org>
Date: Sat Jan 14 19:21:47 2017 +0100
Add build-essential to autopkgtest
commit 82819fea95b13c7608e63056d426f46cfa77765e
Author: Andreas Tille <tille@debian.org>
Date: Fri Nov 4 13:05:01 2016 +0100
Upload to unstable
commit e79fb0a5ee5568b094db8b1bf4a7de22c207b655
Author: Andreas Tille <tille@debian.org>
Date: Fri Nov 4 12:57:28 2016 +0100
Add remark about pristine-tar commit
commit 97b737336b76c25fd31e0cedd95f6bd44a6cfbdc
Author: Andreas Tille <tille@debian.org>
Date: Fri Nov 4 12:56:41 2016 +0100
New upstream version
commit b9d85dc4fc91a7cebf69d26b7c5d8e1bab6756cf
Merge: 5ec9af0 6bed35a
Author: Andreas Tille <tille@debian.org>
Date: Fri Nov 4 12:50:25 2016 +0100
Merge tag '1.3.2' into debian/unstable
HTSlib patch release 1.3.2: bin bug fix, RTLD_GLOBAL plugins
* Corrected bin calculation when converting directly from CRAM to BAM.
Previously a small fraction of converted reads would fail Picard's
validation with "bin field of BAM record does not equal value computed"
(SAMtools issue #574).
* Plugins can now signal to HTSlib which of RTLD_LOCAL and RTLD_GLOBAL
they wish to be opened with -- previously they were always RTLD_LOCAL.
commit 5ec9af017150ea6f3cdccad140876d338bf154e1
Author: Andreas Tille <tille@debian.org>
Date: Thu Sep 1 10:01:47 2016 +0200
Add myself to uploaders, upload to unstable
commit 86cb62bc3b5adeefd334e59af1d7182c9d3eeb46
Author: Andreas Tille <tille@debian.org>
Date: Thu Sep 1 10:00:37 2016 +0200
Fix build on hurd
commit 56a0f1d51f932594eeac0ba4f3647d7c7ff0f485
Author: Andreas Tille <tille@debian.org>
Date: Wed Aug 3 13:20:02 2016 +0200
hardening=+bindnow, upload to unstable
commit 7d0b90b609f7f6ed67da3af3f995fc692f4f8a49
Author: cbk-guest <cbk-guests@scm.alioth.debian.org>
Date: Wed Aug 3 04:24:47 2016 +0300
Autopkgtest added
commit c8c5494bb2e9c1b967dafffa00c0fd54254e005a
Author: Charles Plessy <plessy@debian.org>
Date: Sat May 7 22:20:58 2016 +0900
Step back to 1.3.1-1, ready for backport.
commit 5f4f5732c66ea3526fdc1b436725fb604bdfabea
Author: Charles Plessy <plessy@debian.org>
Date: Sat May 7 22:19:46 2016 +0900
Revert "Breaks: samtools (<< 1.3.1)"
This reverts commit df9bd0e7b1226e93af22cf0c2fb9774a78392ec2.
Only the test suite was incompatible, see https://github.com/samtools/htslib/issues/374
commit 80a1c1c96132ab12f9e893b25709375e4ab143f3
Author: Charles Plessy <plessy@debian.org>
Date: Wed Apr 27 13:34:58 2016 +0900
Current changelog.
commit df9bd0e7b1226e93af22cf0c2fb9774a78392ec2
Author: Charles Plessy <plessy@debian.org>
Date: Wed Apr 27 13:33:35 2016 +0900
Breaks: samtools (<< 1.3.1)
Closes: #822741
commit 68a17aa2cb156363c29638fb62a82fd505477bc6
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 22:28:24 2016 +0900
htslib (1.3.1-1) unstable; urgency=medium
36bf59a Merge tag '1.3.1' into debian/unstable
559f8b4 Remove add_largefile.patch, applied upstream.
7163afb Update symbols file. Missing _vcf_parse_format@Base and fai_read@Base.
c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev.
3b219b8 Enable libcurl.
9101580 Conforms to the Policy version 3.9.8.
-- Charles Plessy <plessy@debian.org> Mon, 25 Apr 2016 22:28:11 +0900
commit 6e232693c7781aa99c7f8e36f0197df670858363
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:48:04 2016 +0900
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 libgnutls28-dev.
3b219b8 Enable libcurl.
9101580 Conforms to the Policy version 3.9.8.
-- Charles Plessy <plessy@debian.org> Mon, 25 Apr 2016 22:19:34 +0900
commit 91015809554ec193961eab3f13a94beba25983e6
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:54:32 2016 +0900
Conforms to the Policy version 3.9.8.
commit 8b1034772c542656a04e2cfd12fea72b18aa5dad
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:46:44 2016 +0900
New upstream release; no new copyright nor license notice.
commit c2c1df36e7e8c0a127091369e43d61e0808c07af
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:43:43 2016 +0900
Build-depend on libcurl4-gnutls-dev and libssl-dev.
commit ac22c29c7808d8e3a32c6e3b9a8e0e7d792e12c7
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:35:54 2016 +0900
Enabled libcurl, Do not enable plugins (no plugins available...).
commit 3b219b8e815f72dfff16b1b1e3f1d637e2745edf
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:31:27 2016 +0900
Enable libcurl.
commit 973e9ac5c28d0a2258d2fa7a0817e68ab97bb1f7
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:26:25 2016 +0900
Updated changelog.
commit 7163afb31095fd3bff811be0360ebe964d90a644
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:17:02 2016 +0900
Update symbols file. Missing _vcf_parse_format@Base and fai_read@Base.
commit 559f8b44bec042eaa7f09f0f4cd07d6cfaf9a016
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:14:26 2016 +0900
Remove add_largefile.patch, applied upstream.
commit b9ed6fcbd856b330c00c14275fa92e9fd419d0b2
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 21:13:04 2016 +0900
A To Do list.
commit c2ca1bfaf91ac531263ee44117c2e56cd942e595
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 20:55:19 2016 +0900
First go back on debian/unstable, otherwise debian/watch is not there.
commit 36bf59a2d342269baca3dd180061ca2de828329b
Merge: 48353e1 0f298ce
Author: Charles Plessy <plessy@debian.org>
Date: Mon Apr 25 20:53:00 2016 +0900
Merge tag '1.3.1' into debian/unstable
HTSlib release 1.3.1: bug fix release, notably error checking
* Improved error checking and reporting, especially of I/O errors when
writing output files (#17, #315, PR #271, PR #317).
* Build fixes for 32-bit systems; be sure to run configure to enable
large file support and access to 2GiB+ files.
* Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370).
Particular thanks to Kostya Kortchinsky of the Google Security Team
for testing and numerous input parsing bug reports.
* HTSlib now prints an informational message when initially creating a
CRAM reference cache in the default location under your $HOME directory.
(No message is printed if you are using $REF_CACHE to specify a location.)
* Avoided rare race condition when caching downloaded CRAM reference sequence
files, by using distinctive names for temporary files (in addition to O_EXCL,
which has always been used). Occasional corruption would previously occur
when multiple tools were simultaneously caching the same reference sequences
on an NFS filesystem that did not support O_EXCL (PR #320).
* Prevented race condition in file access plugin loading (PR #341).
* Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...]
Continue anyway" warning messages (#299).
* Various minor CRAM fixes.
* Fixed documentation problems #348 and #358.
commit 48353e1753735d35b5af30e73e6e0fe091d48ac6
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Feb 8 16:52:01 2016 +0000
move around team upload notice
commit 388bb16abffcf5f34e8743c86386f0982a339b2f
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Feb 8 16:46:49 2016 +0000
dch -r
commit 231557d378815709369d8d304f8e9b64399b425a
Merge: 00bd24c 5632d5d
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Feb 8 16:46:15 2016 +0000
Merge branch 'debian/unstable' of ssh://git.debian.org/git/debian-med/htslib into debian/unstable
commit 00bd24c6605c400099abed1d43dac5253608edae
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Feb 8 16:35:26 2016 +0000
update changelog
commit a0b324148c86b362e4182e12f439d31e76cf2b36
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Feb 8 16:35:17 2016 +0000
run configure step before build
commit 87e9cf5611f41579709e0b24d98ee938a26513d1
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Feb 8 16:34:42 2016 +0000
add patch to run configure
commit 59917d4f15b76213acf32f33fed9bb1e95a92b39
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Mon Feb 8 16:01:46 2016 +0000
add upstream's patch for largefile issue
commit 5632d5d445d77e7dead3b95103113979a47a4c4b
Author: Steffen Moeller <moeller@debian.org>
Date: Sat Feb 6 12:37:55 2016 +0100
Tabix index file format, longer form
commit e25e9710527e2391076eaf9b34b339ca855fe8fe
Author: Steffen Moeller <moeller@debian.org>
Date: Sat Feb 6 12:34:13 2016 +0100
Newly introduced Tabix index file format
commit 67634efa61e785c5d1f5a722d51a806d8313d239
Author: Steffen Moeller <moeller@debian.org>
Date: Sat Feb 6 12:31:44 2016 +0100
Introduced EDAM annotation for TABIX
commit 6c3a0f563a37c855b28500f33a9b7343ba9af320
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sun Jan 31 11:36:50 2016 +0000
set release distribution to unstable
commit 3e3d9a2cbd5e73c45d7fe94b2bd06a131f9a69af
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 12:14:06 2016 +0000
update d/changelog
commit 9eb53943ec8ad6df3633d82a5e7a737c0b940b03
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 12:11:45 2016 +0000
ignore metadata different between tarball and git repo
commit 6cd8493c1fe0330cc448feed2ae877dec70676c3
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 11:58:40 2016 +0000
update symbols file
commit 1d38e31f80051b2fc2c01cb5bbde87441e9f950e
Author: Sascha Steinbiss <sascha@steinbiss.name>
Date: Sat Jan 30 12:11:07 2016 +0000
use secure Vcs-Git
commit d6a8f091a26f6511b0aafb5b8a8fcd1409aa5df3
Author: Charles Plessy <plessy@riken.jp>
Date: Thu Dec 24 13:20:10 2015 +0900
Upstream does not prefix tags with 'v'.
commit b333524c104fff71e2683a9f8408fb5f061ebbb7
Author: Charles Plessy <plessy@riken.jp>
Date: Thu Dec 24 13:17:51 2015 +0900
New upstream release; corrected path to a copyright statement.
commit 68e6f6c1b6dd413a13f61eb8ca174a503da8e394
Merge: e6d7e9d 87141ea
Author: Charles Plessy <plessy@riken.jp>
Date: Thu Dec 24 13:14:35 2015 +0900
Merge tag '1.3' into debian/unstable
HTSlib release 1.3, plugins, libcurl, CRAM v3.0, bug fixes
* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
and FTP, when HTSlib is configured to use libcurl for network file access
rather than the included basic knetfile networking.
* HTSlib can be built to use remote access hFILE backends (such as iRODS
and libcurl) via a plugin mechanism. This allows other backends to be
easily added and facilitates building tools that use HTSlib, as they
don't need to be linked with the backends' various required libraries.
* fai_build() and samtools faidx now accept initial whitespace in ">"
headers (e.g., "> chr1 description" is taken to refer to "chr1").
* tabix --only-header works again (was broken in 1.2.x; #249).
* HTSlib's configure script and Makefile now fully support the standard
convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
as needed. Previously the Makefile listened to $(LDLIBS) instead; if you
were overriding that, you should now override LIBS rather than LDLIBS.
* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.
commit e6d7e9d1b42d164f3e74b0b903a30a9286f1f29b
Author: Andreas Tille <tille@debian.org>
Date: Wed Dec 9 17:00:51 2015 +0100
Upload to unstable
commit eb12aa09b789e0e4cd22b00d02eda97c614ac66e
Author: Andreas Tille <tille@debian.org>
Date: Wed Dec 9 17:00:39 2015 +0100
Verified Mayhem bug report which is solved in this version
commit c1eaca0fbae93fe7515728670acae76a256fa641
Author: Andreas Tille <tille@debian.org>
Date: Wed Dec 9 16:59:51 2015 +0100
Fix lintian override
commit 57b6def36eb632fb547a182b7858a08ac88eed94
Author: Andreas Tille <tille@debian.org>
Date: Wed Dec 9 16:54:31 2015 +0100
More verbose description vor -dev and -test package
commit 5fb0d2db2c057243309f5d80e502af04ebfc963c
Author: Andreas Tille <tille@debian.org>
Date: Wed Dec 9 16:43:31 2015 +0100
Define PATH_MAX
commit 04d85d9d1cf0e25e41a3b606b2bb5f819943654c
Author: Andreas Tille <tille@debian.org>
Date: Tue Jul 28 12:13:17 2015 +0200
In this repository the 'v' in front of the version number needs to be left out ...
commit d4dbf8d886899adb6d13d80b2073da94801947a7
Author: Andreas Tille <tille@debian.org>
Date: Tue Jul 28 12:06:57 2015 +0200
Add README.source to explain the workflow of this Git repository
commit 12251926b9d0265738d701bb0add6fe9d070ccb3
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 13:56:39 2015 +0900
htslib (1.2.1-1) unstable; urgency=medium
0662716 Merge tag '1.2.1' into debian/unstable
084f27d Install NEWS as upstream changelog.
316fb96 Override a Lintian false positive.
3363679 Clean test directory.
69bf167 Corrected a typo in tabix description.
-- Charles Plessy <plessy@debian.org> Mon, 25 May 2015 13:35:03 +0900
commit 69bf167de34bc0c8a192add5f6748fe8d8888ab6
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 13:33:56 2015 +0900
Corrected a typo.
commit 33636795f14d13134d121af3ce4061e7aabfcc49
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 13:31:02 2015 +0900
Clead test directory.
commit 316fb961360707c2683cd5fc9a34b0582d13bcbd
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 13:25:48 2015 +0900
Override a Lintian false positive.
commit 084f27db8fe9132424e2c40db38f6abee253dfe9
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 13:05:28 2015 +0900
Install NEWS as upstream changelog.
commit e047ee4353bc0305db1db1c3477c3162c3ec9142
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 13:00:44 2015 +0900
New upstream release; no new copyright nor license statement.
commit 4fc92f5aab173eedbefacef6a2514a5c2d903449
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 12:40:23 2015 +0900
Update symbols file. Note that there are missing symbols.
#MISSING: 1.2.1# cram_byte_array_stop_decode_char@Base 1.0
#MISSING: 1.2.1# cram_external_decode_block@Base 1.0
#MISSING: 1.2.1# cram_external_encode@Base 1.0
#MISSING: 1.2.1# download_and_open@Base 1.0
commit 0662716ffdbffe1d3606a8182a0ce33f4edd81c0
Merge: 9750123 26229a3
Author: Charles Plessy <plessy@riken.jp>
Date: Mon May 25 11:44:54 2015 +0900
Merge tag '1.2.1' into debian/unstable
HTSlib patch release 1.2.1, reinstated hts_file_type()
commit 97501235644584386682e107722cd50a8bf4c7a8
Author: Charles Plessy <plessy@debian.org>
Date: Sun Oct 5 09:39:24 2014 +0900
Current changelog; not sure to upload or not.
commit ac4c98ad382fad693029cc85095b1dcb1db95a91
Merge: 15eac2b 56d50b2
Author: Charles Plessy <plessy@debian.org>
Date: Sun Oct 5 09:34:38 2014 +0900
Merge branch 'develop' into debian/unstable
commit 15eac2bd29eccdbabc429b0281e3f65e99a18859
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 24 21:29:59 2014 +0900
htslib (1.1-1) unstable; urgency=medium
1357fbd Merge tag '1.1' into debian/unstable
87549cd Updated symbols file. One symbol is missing.
873ea9b Removed orphan paragraph in machine-readable copyright file.
49de2b9 Allow parallel build.
7fe3bb5 Normalise control file (VCS-Browser, Pre-Depends).
0e5e9e6 Conforms to Policy 3.9.6.
-- Charles Plessy <plessy@debian.org> Wed, 24 Sep 2014 21:24:11 +0900
commit 0e5e9e6266c16e07eb75638c486c5589721f5d2d
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 24 21:23:51 2014 +0900
Conforms to Policy 3.9.6.
commit 7fe3bb5d5137eff0b299ab81232f0aaf766ef884
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 24 21:22:36 2014 +0900
Normalise source package control file (VCS-Browser, Pre-Depends).
commit 49de2b98046745dfe4fdd121ea34413ebb42164e
Author: Charles Plessy <plessy@debian.org>
Date: Wed Sep 24 21:21:24 2014 +0900
Allow parallel build.
