0141e47ab9ca92cd2aeb6d573440d689bbfdf327 to 103be52531bf6c4303e463ecfff0d5a201f6708c · Debian Med / htslib · GitLab

Commits on Source 1058

1f1e3f63 Merge version number and soname bump from master
Aug 15, 2014
1903fd40 Set explicit REF_PATH to make tests self-contained
Aug 20, 2014
b6934ff8 Force nul termination of the kstr holding the CRAM index so that
Aug 26, 2014
6c6c75b9 Make hts_idx_push no longer return 0 after the first unmapped read. This fixes idxstats
Aug 26, 2014
3fe4cf8e Ensure hand-made kstring is NUL-terminated
Aug 26, 2014
89e267a4 Ensure items to be installed are built and up-to-date
Aug 26, 2014
546bfcb5 vcf: Output "." not "nan" in scalar INFO fields
Aug 27, 2014
6af42b15 vcf: separate header lookup from field getter
Aug 30, 2014
410cf54d Merge pull request #127 from broadinstitute/broad_header_lookup
Sep 01, 2014
ebbad4b7 Merge pull request #124 from dpryan79/develop
Sep 01, 2014
830ea739 faidx API to access sequence stats
Sep 03, 2014
20558bc9 bcf_get_info_values: Return correct INT8 and INT16 missing value
Sep 08, 2014
cf4eab09 Minor documentation update
Sep 09, 2014
575be149 Correct reference lines
Sep 09, 2014
3f308835 Removed the .gz, .Z, .sz etc suffix searching when looking for reference files.
Sep 12, 2014
d25c678a Remove the | from the default REF_PATH.
Sep 12, 2014
061cd10a Minor speed increases to cram_byte_array_stop_decode_init and
Sep 12, 2014
6454bd4e Added a range coder (order 0 and 1) plus support for LZMA if compiled
Sep 15, 2014
94cf60ac Tweaks for specifying version number. Now accepting version 3.0, and
Sep 15, 2014
3d3f4001 Updated the version checks to lop off major/minor components rather
Sep 15, 2014
37f42cd4 Fixed BETA codec so that it honours beta offset value for zero length
Sep 15, 2014
1de851bb Bug fix to the external decoders. If there is an attempt to decode 0
Sep 15, 2014
0d394594 Added support for more codecs, as part of refactoring how data is
Sep 15, 2014
672f0798 Major refactoring of the way CRAM handles external blocks.
Sep 16, 2014
8210cf35 htslib (1.0-2) unstable; urgency=medium
Sep 16, 2014
100f2d05 Removal of a couple memory leaks added in the restructing of the last
Sep 17, 2014
b73b5274 Bug fix of use of TAG_ID macro and k vs key in hash for auxiliary
Sep 17, 2014
5a840dae Modified the thread pool to use as few threads as possible. The
Sep 17, 2014
6929b9c7 Bug fixed scramble -x as it was not correctly setting the RI data
Sep 17, 2014
ef7eeed6 A mishmash of changes for CRAM v3.0 (not yet the default output
Sep 17, 2014
a2542855 Minor gcc warnings fixups.
Sep 17, 2014
2e298614 Added support for compressed SAM headers.
Sep 17, 2014
c7f8feec Final part of Staden io_lib's commit r3686.
Sep 17, 2014
6d01daaa Initialise refs_t ->ref_id in refs_load_fai(). This has no bearing on
Sep 17, 2014
fa6011a5 bgzf: Write plain gzip files if is_gzip set
Sep 17, 2014
22718e5e Added CRC32 to the blocks and containers.
Sep 17, 2014
3ca319f5 Fixed the file format detection code so it handles CRAM v3.0 magic
Sep 17, 2014
10958ff8 Changed the hts_open code to support "C" as a format mode as well as
Sep 17, 2014
bf2d07c5 Fixed bam_construct_seq to cope with qual being NULL.
Sep 17, 2014
efa6537a Removed the previous "c" vs "C" hack and added a proper option parser
Sep 18, 2014
1965be21 Fixed generation of MD and NM tags in cram_decode_seq() when using a
Sep 18, 2014
b56f540e Added a special case for setting the reference. When converting from
Sep 18, 2014
ad3c4c56 Cope with cram_compress_slice failing. We were unwinding the stack
Sep 18, 2014
1ef04ee8 Removed the need for -DSAMTOOLS when compiling CRAM.
Sep 18, 2014
b5ecdf7f (Commented out): ugly auto-configuration of HAVE_LIBBZ2 and
Sep 18, 2014
a223cae8 Added multi-threading support for reading and writing CRAM.
Sep 18, 2014
4835f533 CRAM_OPT_VERSION now works (and only works) on an open file
Sep 18, 2014
f5aeebbb bgzf_open(..,"g") for compressed gzip output, as opposed to BGZF
Sep 19, 2014
ac13591d Added SAM_RGAUX as another column identifier to allow for tools that
Sep 19, 2014
2f10ff9e Removed defunct comment.
Sep 19, 2014
0cdb7b1a Minor tidyups to prevent some clang warnings.
Sep 22, 2014
dcefe5b7 Don't install libhts.so.1 as a man page
Sep 23, 2014
5a0ee032 Release 1.1: various minor bug fixes
Sep 23, 2014
f2080d5c Merge version number bump from master
Sep 23, 2014
1357fbd6 Merge tag '1.1' into debian/unstable
Sep 24, 2014
be365db8 New upstream release, no new copyright nor license notice.
Sep 24, 2014
87549cd9 Updated symbols file.
Sep 24, 2014
873ea9b6 Removed orphan paragraph.
Sep 24, 2014
49de2b98 Allow parallel build.
Sep 24, 2014
7fe3bb5d Normalise source package control file (VCS-Browser, Pre-Depends).
Sep 24, 2014
0e5e9e62 Conforms to Policy 3.9.6.
Sep 24, 2014
15eac2bd htslib (1.1-1) unstable; urgency=medium
Sep 24, 2014
5b98adcd Added regidx API which should replace bcf_sr_regions at some point
Sep 25, 2014
f4b4b617 Clean after regidx init failure; fixed build dependencies
Oct 01, 2014
d27ae83d Fix in bcf regions which in some situations would skip first
Oct 01, 2014
d2cb7bac regidx: simple file format autodetection
Oct 01, 2014
eecc982e Fixes for handling range requests while also multi-threading.
Oct 01, 2014
d6cdff67 Fix for FSECONDARY reads; do not link into PNEXT/RNEXT.
Oct 02, 2014
c116e113 add new test-regidx binary to .gitignore
Oct 02, 2014
a0e35e03 Formatting fixes for man page
Oct 02, 2014
db774cc5 Merge pull request #136 from mcshane/feature/ignore_test-regidx
Oct 02, 2014
9eb4bed0 Removed various small memory leaks.
Oct 02, 2014
14a4a81f Return type of bgzf_getc is int, not char
Oct 03, 2014
56d50b27 regidx: use size_t, not ssize_t
Oct 03, 2014
5ebf9b24 Fix regidx.o dependencies and htslib.mk; alphabetise
Oct 03, 2014
ac4c98ad Merge branch 'develop' into debian/unstable
Oct 05, 2014
97501235 Current changelog; not sure to upload or not.
Oct 05, 2014
effc6fdf Merge man page formatting fixes
Oct 06, 2014
912a7d09 Support for Type=Character, in htslib same as Type=String
Oct 06, 2014
34f8089d VCF header editing speedup for large number of ref sequences
Oct 10, 2014
9d01cd60 New bcf_copy API
Oct 14, 2014
432a2240 Split off the rans_byte.h portion of rANS_static.c back into its own
Oct 15, 2014
b5d11c3b Added copyright notice.
Oct 16, 2014
43f2d111 Remove -DSAMTOOLS vestiges
Oct 16, 2014
24c86999 Fix cram/rANS_* dependencies
Oct 16, 2014
233e1592 Merge CRAM v3 updates (PR #132)
Oct 16, 2014
abd1efb3 Add htsFormat and format-detection API functions
Oct 17, 2014
bf909d66 Removed old hts_file_type() API and replaced it with the new htsFormat;
Oct 20, 2014
7c42dccd Clean up, is_compressed and is_cram no longer necessary
Oct 21, 2014
eda497bd Do not use 0x80 & co for missing alleles
Oct 21, 2014
3e24dfd2 Do not load remote index if already exists locally
Oct 21, 2014
529ca880 Use htsFormat to replace htsFile's is_foo flags
Oct 22, 2014
41ab01b2 Add htsfile utility
Oct 22, 2014
5dec96ba Amended the compression level checking code in cram_dopen() to follow
Oct 27, 2014
b0df3d15 Fix in bgzf's gzip reading plus added a test for this
Oct 29, 2014
9c510fb5 bcf_translate: Be aware of gaps in BCF headers
Oct 29, 2014
b28efa4f In a bid to keep the DEBUG_printf line potentially printing up the
Oct 29, 2014
a98d88fd Fix a bug where hts_set_fai_filename() didn't pass this through to
Oct 29, 2014
9e844e0b Fix bug spotted by valgrind when running "./test_view -D
Oct 29, 2014
7a13d832 Fixed an error found via valgrind of test_view -D c1#pad1.tmp.cram.
Oct 29, 2014

958 additional commits have been omitted to prevent performance issues.