[med-svn] [htslib] annotated tag debian/1.1-1 updated (f65dde0 -> 4d788b9)
Charles Plessy
plessy at moszumanska.debian.org
Wed Sep 24 12:43:29 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag debian/1.1-1
in repository htslib.
*** WARNING: tag debian/1.1-1 was modified! ***
from f65dde0 (tag)
to 4d788b9 (tag)
tagging 15eac2bd29eccdbabc429b0281e3f65e99a18859 (commit)
replaces 1.1
tagged by Charles Plessy
on Wed Sep 24 21:42:54 2014 +0900
- Log -----------------------------------------------------------------
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 at debian.org> Wed, 24 Sep 2014 21:24:11 +0900
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1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=MFye
-----END PGP SIGNATURE-----
Charles Plessy (67):
Listed copyright and license notices.
Draft package.
Merge branch 'develop' into debian/unstable
Documented cram/*, collated copyright notices for works under the MIT license.
Do not build a htslib binary package: there is not htscmd program anymore.
Install in and from debian/tmp.
Merge branch 'develop' into debian/unstable
Corrected paths.
Make the package multi-architecture.
Align package name on soname.
Align package name on soname.
Clean test directory before packaging it.
Submitted ITP #729282 with the current package descriptions.
Merge branch 'debian/unstable' of github.com:Debian/htslib into debian/unstable
Uses pristine-tar and may use git-buildpackage.
Upstream tag 0.2.0_rc3.
Watch GitHub.
Mangle the upstream name, so that the tarball has a correct version number.
Empty symbols file, to be populated by Debhelper.
fakeroot dh_makeshlibs | patch -p0
Removed minor number.
Corrected length of lines.
Make dh-exec files executables, since we are using the 1.0 source format.
Pass dpkg build flags.
Make libhts-dev depend on libhts0.
Prospective VCS URLs (Alioth is currently down…).
htslib (0.2.0~rc3-1) unstable; urgency=low
Override PACKAGE_VERSION to avoid tags with a slash in the name.
Finally use the 3.0 (quilt) format in single-debian-patch mode.
Merge branch 'develop' into debian/unstable
Changelog for work in progress.
Updated symbols file.
Merge remote-tracking branch 'upstream/develop' into debian/unstable
Refreshed changelog after pulling new upstream tag.
New upstream tag; no new copyright nor license statement.
Adjusted substitution variables following dpkg's warnings.
Use the Debian as package version.
Updated the changelog.
Removed debug command accidentally introduced.
Merge branch 'develop' into debian/unstable
Merge branch 'develop' into debian/unstable
New upstream tag; updated changelog.
Updated Symbols file.
Merge branch 'develop' into debian/unstable
Updated symbols again.
Merge branch 'master' into debian/unstable
New upstream release; no new license notice.
Build on the master branch.
Updated symbols file.
New major version (libhts0 -> libhts1).
Remove Debian revision from symbols version.
Pass multiarch path to Make. Install pkgconfig file.
Replace the old tabix package (from the tabix source package).
Dynamically link tabix and bgzip.
Prepare changelog.
Polish descriptions.
Statically link tabix and bgzip for the moment.
htslib (1.0-1) experimental; urgency=low
htslib (1.0-2) unstable; urgency=medium
Merge tag '1.1' into debian/unstable
New upstream release, no new copyright nor license notice.
Updated symbols file.
Removed orphan paragraph.
Allow parallel build.
Normalise source package control file (VCS-Browser, Pre-Depends).
Conforms to Policy 3.9.6.
htslib (1.1-1) unstable; urgency=medium
-----------------------------------------------------------------------
omits 255f66f htslib (1.1-1) unstable; urgency=medium
omits 6dcb302 htslib (0.2.0~rc3-1) unstable; urgency=low
omits 247dab5 Initial empty branch.
adds 3860d63 initial checkin
adds 47191a7 finish parsing ## lines
adds 2e0e641 header parsing finished (not well tested)
adds aac04c8 towards parsing VCF
adds 546e607 BCFv2 quick reference
adds fe0041e code backup
adds b17f2c5 a bit code restructuring
adds 7e33530 encode up to the INFO field
adds 185b5f5 VCF=>BCF, up to QUAL
adds 973a1be bcf->vcf, up to FILTER
adds aa7b673 bcf->vcf, up to INFO
adds 6caad03 change long to int32_t
adds 722124a towards parsing genotype fields (unfinished)
adds dde5251 a little code cleanup
adds 5cdfa18 parse genotype fields; not tested yet
adds 44b011d restructure the code a bit
adds e667943 to restructure decoding
adds 3274571 restructure decoding
adds d6028ed working on printing genotypes; not working yet
adds ee9bc0d fixed one bug, more to fix
adds 07b4746 working on a toy example!!!
adds b3e623b another bug fix
adds c2da32c add a very simple CLI for testing
adds 1003534 if PASS is not in the hdr, add it
adds 6959b7c use two memory buffers to fix a bug
adds d663b02 clean bill by valgrind on a toy example
adds 4608878 move the memory buffer to the header
adds 29015d5 bugfix: extra byte for string
adds c70504d read seq dict from an external file
adds 9dc290c finished text-in-text-out
adds 4c0f791 code backup
adds fd1f4f4 bcf->vcf without inferred information
adds 7d7ccc4 do not compute inferred info during vcf->bcf
adds 1badf87 separate shared and individual annotations
adds df8eff4 rename variables
adds 2fffb33 added simple cmd interface
adds 45be8f4 separated the main function; added Makefile
adds baaa3fb add external seq-dict to the header
adds a9a6ae4 added git ignore
adds 341a947 updated the quick reference
adds 976e97f bugfix: -l not working; corner case of Number=.
adds 7dbaa13 bugfix: segfault given Number=.
adds 75db452 when -l is in use, use binary output
adds 791efdf parse Flag type
adds f776393 bugfix: in case of no FORMAT
adds a6d5876 added CNL to the example
adds 7b74c08 clarified quick reference
adds 801bb84 more consistent Flag; code clean up
adds 9fedbbc do not keep '\0' in sample strings
adds 81ee0f0 cleanup
adds 8901681 allow arrays longer than 128
adds 8bf3593 bugfix: missing "," in ALT
adds c62466e use three header hash tables instead of one
adds 5ab4fd8 rename variables
adds ceeff19 added line counting
adds caccb02 routine to unpack FORMAT
adds 4081e7f collect site allele count
adds 0860358 fixed a memory leak
adds d1ac9b6 supposedly faster VCF parsing
adds ac25a3f minor
adds 3f59614 can be compiled with g++
adds 6a3a99a bugfix: str in GT not encoded properly
adds 3127025 bugfix: incorrect float
adds 85d1be2 move alloca() upwards
adds b418823 code backup; not working!
adds ba388a1 parse n_sample from record lines
adds 634d84d back to work
adds b37f9f8 encode GT
adds bb530e2 phasing info stick to the allele behind
adds b53a61c updated BCFv2 spec
adds cd33690 merge REF and ALT
adds d0cab9e added GT encoding
adds 92290e0 updated to the latest BGZF
adds df356d2 bugfix: prematured output in bgzf-mt
adds 3c2af63 g++ errors in bgzf-mt
adds 9dc247b prepare to add sam parsers
adds 9b66553 separate file I/O
adds 55d181a use hts.{h,c} in vcf
adds 0c7db5d replace vcf_verbose with hts_verbose
adds c644e21 BAM I/O, SAM output; not tested
adds 72432b3 compiling err/warning from g++
adds 530ba16 create separate directory
adds f233c19 rename api to htslib
adds feb86e1 added sam interface; not working
adds df979ba bugfix: wrong returned value from knet_seek()
adds b463806 code backup; NOT compiling
adds 6d004ce compiled, but certainly not working
adds a4f0bdf working, up to QUAL
adds b8f1d57 SAM parser works on a toy example
adds 56d7ddb report line number
adds 6375f0c use hts_getline() to keep line number
adds b42cc73 bugfix: wrongly parse B arrays
adds 32561b4 added a SAM example
adds d8ddcc0 do not check CIGAR if CIGAR==*
adds e546ed8 bugfix: uninitialized numbers
adds 75e3bd9 bugfix: compute "bin" in bam
adds 9532488 code backup
adds b954f55 added comments
adds b09fcae code backup
adds f9cb9cc code backup
adds 93df7a9 minor changes
adds e3e6d3b code backup
adds eab97ae separate indexing from hts.c
adds d27cec6 bam index interface
adds a631896 index load; bugfix: wrong offset of last chr
adds 4dd932e code backup
adds bb83110 add region parser (not tested)
adds b8733af code backup
adds 20ba14c indexing apparently works for BAM
adds 144b7ef bugfix: one extra record from random access
adds 7ec64b1 fix C++ compiling errors and warnings
adds 18ac806 code cleanup
adds b733d9c removed sam_hdr_t::has_SQ
adds 6053079 added the pileup/mpileup interface
adds 2244809 fixed g++ warnings
adds b6f6440 automatically figure out the index file name
adds 20c7222 forgot to add Makefile
adds 99f4547 expose bgzf.h
adds 6e20b48 bamshuf: shuffle BAM
adds f06e1e3 added bam2fq
adds c9bda2f System may have an <endian.h>; merge to hts.h
adds 8efb052 fixed gcc warnings
adds 962a3a5 added simplified stdint.h, in case it is missing
adds b16b96b bam2fq: output SE reads in the PE mode
adds 16275c3 output the number of reads
adds 0313740 bugfix: bamshuf not working when collision
adds 09ee5a0 make BCF APIs similar to BAM APIs
adds b92ee1d added Description to PASS
adds 9bf881e detailed vcfview cmd prompt
adds 32f4466 bam2fq: change the option name
adds c69050d generalize the BAM index
adds 79e477b unified index seems to work; optimization needed
adds 1426dd5 merge a small bin to its parent
adds 13c21f2 fixed a couple of warnings
adds ba50fb3 changed magic
adds 9aabfc0 bugfix: parent merging not working
adds fb88ba9 reduced the min chunk size
adds bfcfcda BCF2 index; compiled but not working
adds e8ad97c BCF index working on a toy example
adds 2d1090c allow longer arrays
adds df19476 allow missing binary index
adds 20e7996 wrong n_lvls
adds e4813e9 bugfix missing string not printed properly
adds 0044a03 avoid printing "\0" in the header
adds 1b6136c replace 0x7F800001 with bcf_missing_float
adds 07790f2 stop if not sorted
adds 51542f0 code backup; NOT working
adds bc5a869 a bit code cleanup
adds 1291adc code cleanup
adds b9b4afa bugfix: hts index not working when n_seq is unknow
adds 09db228 CLI for tabix
adds 9b5fcbd tabix apparently works, at least on toy examples
adds 6ed05de added an example for tabix
adds 73afb81 format of the new index
adds dc46744 minor change to the index description
adds eda81c1 fixed a few g++ warnings
adds 67f0b9d added command-line help
adds f355744 added a brief README
adds cc7b3c0 more flexible about the '\n' and '\0' in hdr
adds f73f662 bugfix: wrong integer packing
adds 97dbfb0 change the meaning of l_shared (in line with GATK)
adds d5b55bc output a subset of samples
adds 3cb1f4b allow to drop all individual information
adds ffc8d65 smart sample list
adds 9ea927a bugfix: missing values are not filled sometimes
adds 38296d0 new indexing algo/fmt; NOT working yet
adds 0fd291d BAM indexing works again on a toy example
adds 08c8bb5 bugfix: bin 0 is not sorted
adds 112176a a bit code cleanup
adds 73bc25e bugfix in the new index; containing dbg code
adds be1e4c1 bugfix
adds c6e9c5f using -O2
adds cf0da03 bugfix: update_loff() run twice
adds a9388b0 handle unmapped aln in SAM
adds 03ec23b halve HTS_MIN_MARKER_DIST; updated doc
adds 2954e1d declare bcf_fmt_sized_array() in the header
adds b1512c1 unpack bcf1_t; NOT WORKING yet
adds f71e2c1 nothing
adds d185fc6 declare bcf_unpack in the header
adds b35d09a Merge pull request #2 from arq5x/master
adds 200b841 generating vcf from bcf_dec_t; to remove old code
adds c1c36bf removed old vcf_format1() code
adds 3110062 bugfix: a typo
adds cac07ac a little bit code simplification
adds 8fe0f48 make bcf_unpack() more flexible
adds 8d62aaf changed function names
adds 5683533 added a little doc
adds 1f23f2b migrate sam2break.d to htslib
adds 87ab8c0 abreak is working!
adds 2633148 better help
adds 6c7bfff vcf<->bcf is pretty mature now
adds 92a96c9 compatible with tabix index
adds 49b0749 bugfix: vcfview -G failing due to recent changes
adds 6d05f18 API to test if a record is a SNP
adds 9b6b318 added BAM aux functions and bam2bed
adds 1fa4c89 bugfix: invalid memory access (fixed by petr)
adds 5b98268 vcf: add "PASS" before anything else
adds faeb779 clarify the BCF2 document
adds cffe2b6 clarify that BCF2 is BGZF'd and little endian
adds bb3e0b9 Experimental implementation of vcfcheck (non-functional)
adds f58b777 Fill sequence dictionary from tabix index if contigs not present in VCF header. Synced reader basically working. (No alleles detection yet.)
adds a564bfe Functional implementation of synced reader including allele checking
adds 33b6f03 Collect Ts/Tv by AF
adds d133a54 Synced reader can collapse sites by variant type; new API call set_variant_types
adds c8f1555 Invalid read fix in hts_itr_query; Unsafe loop limits fix in vcf_parse1
adds 897f9d1 First plot-vcfcheck skeleton
adds 8999bf8 Removed hacky work around, tabix seems to be fully working now
adds 5508b9c Merge branch 'master' of github.com:pd3/htslib
adds 8de0693 Calculate AC,AN on fly if not in INFO; allow calling bcf_unpack() repeatedly without redoing the work; plot graphs using matplotlib; bugfixes
adds 621aeb7 Calculate AC,AN on fly if not in INFO; allow calling bcf_unpack() repeatedly without redoing the work; plot graphs using matplotlib; bugfixes
adds 5e236ad Use matplotlib and pdflatex to create summary slides
adds 17acc9e More stats: indel distribution and substitution types
adds b364964 More stats: SNP and indel counts by AC
adds dce457b create_pdf: Switched from slides class to memoir
adds 5fb5791 More stats: frameshifts ratio; bug fixes
adds 5dfae19 Merged github.com:pd3/htslib
adds 2d16106 Documented the synced reader; More stats for vcfcheck: genotype concordance; Bugfixes
adds c201d5a More vcfcheck stats: Ts/Tv and nHets by sample
adds 09f4cb6 Another vcfcheck stats: NRD by sample
adds c251364 Fix in per sample stats; Minor cosmetic improvements of plots
adds dff6a2b Sample list from file or command line; Handle missing GTs in calc_ac and init_iaf; Documented plotting
adds 07ae6f2 Changed NRD output
adds 2f3e234 New option --split-by-ID for known vs novel stats
adds 23a1aa4 Fix in calc_ac for missing GTs; Number of MNPs and other events in the summary table
adds 3a3c878 Always check INFO/AC,AN for by AF; TsTv by Qual stats
adds 633f436 Depth distribution stats
adds 22543d6 Fixed typo, open with w instead of r
adds c2a68d3 Fixed typo, check i-th ALT instead of 1st in set_variant_types
adds 283cefe Synced reader and hence vcf*tools now work also with bcf2
adds 0a200b4 r198: changed the BCF2 magic to BCF\2\1
adds c8bdd76 r199: support retrieving reads w/o coordinates
adds c63f2ec Merge remote branch 'main/master'
adds 46a866f Fix function prototypes for knetfile and bgzf to match system read and write.
adds b8014e6 Use off_t and lseek rather than the 64 alternatives as this is more portable.
adds 7be5993 Merge remote branch 'mp15/misc_improve'
adds a0dab49 Cumulative commit with many changes, including: - symlinking htscmd enables abbreviated commands - header manipulation routines in htslib/vcf.* - test suite for checking consistency - improvements and new features in existing vcf*commands - skeleton of vcfmerge (not fully functional yet) - bugfixes
adds f56ce9a Bug fix: variant type not checked in the absence of --collapse option, this affected all vcf* commands
adds 2253b7e Changed order of underscore escaping and line breaking to prevent loss of escape characters
adds e9a0809 In calc_ac check added for different BCF_BT_INT* types; New trim_alleles method
adds 97e758e Fix in variant type recognition: distinguish indels from complex events
adds e79542f Plotting Hets vs Homs instead of plain Hets; Sanity check for FS section header
adds 39d404b Add missing contigs to the header permanently
adds 55157de Removed repeated call of bcf_unpack_fmt_core in vcf_format1
adds 922e9c1 New API routine: remove_alleles; get_fmt_ptr
adds 626d874 New API routine: remove_alleles; get_fmt_ptr
adds 6b262e1 New API routine: remove_alleles; get_fmt_ptr
adds 1302894 Do not attempt to read directories in bcf_sr_set_samples
adds 6f59a40 Use uint64_t for DP stats. On behalf of Chris: plot-vcfcheck can now merge per-chromosome vcfcheck files.
adds 8c3471e Fixed a typo which rendered -n <cnt> ineffective.
adds 6c66de8 New -C, --complement option for vcfisec. bcf_seqnames now returns chromosomes in correct order
adds e29e94c Temporary changes
adds f0e6fec tmp save
adds 5a57ff4 GT merging now functional
adds aaaa18b Sanity check allow output from both vcfcheck and plot-vcfcheck -m
adds 5c19e1f Allow missing values in lists in VCF output
adds 3563310 Most features of vcfmerge functional now.
adds 1bc5f6f Merge branch 'master' of github.com:pd3/htslib
adds 2d9a6cb merge_format_field: fix in setting missing values
adds 3b64be1 Fixed memset error in vcfmerge
adds 8055bae Fix in merge_alleles (expand REF if necessary); Normalize local copy of ALT,REF
adds ab2a27c plot-vcfcheck: New --rasterize option for fast PDF rendering
adds 755907e plot-vcfcheck: fixex merging of per-sample stats
adds 095c00c vcf_parse1: error recovery on missing FILTER/INFO/FORMAT tag definitions
adds e25fb12 vcfcheck: New stats and graph, allelic r2 by AF
adds ebc767a plot-vcfcheck: fixed forgotten .pdf extension string
adds 959db8d Merge pull request #1 from samtools/master
adds 76bc90d Fix signed return going into unsigned variable
adds 7dfbbe8 Merge remote branch 'remotes/mp15master/master' into develop
adds d000f83 plot-vcfcheck: removed forgotten debugging comments; merge of allelic r2 column in GCsAF
adds 6a903ed plot-vcfcheck: -T option to set PDF title; minor improvements in various plots
adds e207c50 htscmd: fall back to default name when named non-standardly
adds 5258aaa vcfcheck: singletons by sample and multiallelic SNPs stats
adds 60c60d8 plot-vcfcheck: new -s switch; several new graphs and table values
adds 4d7c161 plot-vcfcheck: Added missing legend into SNP/indel counts by AF graphs
adds 92217e5 vcf.c: strip newline from the last sample in BCFs
adds 3d24cd5 plot-vcfcheck: Fix in merging per-sample average depth - average, not sum
adds 1208a13 Merge remote branch 'remotes/pd3master/master' into develop
adds 3894559 htslib/vcf.c: Set length of on-fly added chromosomes to max signed int; Removed deprecated header parsing code.
adds b238605 plot-vcfcheck: zoomed y-range for ts/tv by sample graph
adds 420881b htslib/vcf.c: free unused records, fixed a small memory leak
adds 6185a7b vcfcheck: New -t option
adds 145e599 vcfcheck: --debug outputs to stdout rather than stderr and the output parsable
adds 85850c1 plot-vcfcheck: Prevent division by zero in FS merging
adds 88ee406 plot-vcfcheck: Escape all underscores summary.tex
adds 58e328b Fix in treatment of haploid Number=G tags. New category for structured header lines such as ALT=<ID=..>. Temporary solution to missing values in vectors: TODO!
adds fc41e37 Make nucleotide tables const
adds 31e76af Amend .gitignore to ignore produced binaries
adds 1b554a4 r200: keep read index in bam1_t
adds 2340eda Merge branch 'master' of github.com:samtools/htslib
adds ba60d62 Merge remote-tracking branch 'upstream/master'
adds db4acc0 Add .gitignore for LaTeX to doc directory
adds 781eb46 Merge remote branch 'remotes/mp15master/master' into develop
adds 1177f60 Merge branch 'develop' of github.com:samtools/htslib into develop
adds e179827 New tool: vcfquery. (TODO: sample columns)
adds 0eb64b0 calc_ac in vcfutils: return when AC present in header but absent in the line
adds d38cede New tools: vcfquery, vcffilter (SOM)
adds e918535 vcffilter: Allow fixed threshold filtering of annotations which are not used in SOM
adds 51ddaa0 vcffilter: added check if supplied annotations are unique
adds a63f58a vcfquery: print header only when requested
adds 2afe338 vcfcheck hotfix: Handle properly sample stats, cases where AC,AN are present in the header but not in the lines
adds 1f12f86 Fix handling of legacy tabix indexes with empty dictionary.
adds c067874 Merge pull request #7 from mp15/master
adds 882af47 Merge branch 'develop' of github.com:samtools/htslib into develop
adds e248154 gtcheck: New tool, initial commit
adds 24fd203 vcfquery: Read multiple VCFs from a file.
adds d6e7be5 htslib/vcf.[hc]: Keep ID separately from the alleles block. Renamed synced_bcf_reader data structures and functions.
adds aa32b80 Added faidx into htslib
adds fac764a Merge branch 'develop' of git://github.com/samtools/htslib into develop
adds bda1c25 Merge branch 'develop' of github.com:samtools/htslib into develop
adds 30219e0 vcffilter: allow filtering of split VCFs with -r
adds ad34679 vcfquery: forgotten open call with -l
adds a2d192f gtcheck: better output file names with -p dir/ prefix.
adds 1f32fe6 gtcheck: Print header in the "-s and no -p" mode.
adds 31c3a44 norm indels: backup commit
adds 0a596c5 Merge remote branch 'remotes/origin/develop' into norm-indels
adds 4987a94 vcfnorm: New command for normalizing and left-aligning indels.
adds 5f16541 Merge branch 'develop' of github.com:samtools/htslib into develop
adds 17765c6 vcfquery fix: throw an error when no VCF given with -l.
adds 60f4eac vcfgtcheck fix: added the command into main()
adds e8e4d49 Synced VCF/BCF reader and most of the vcf*tools now read from stdin. Speedup in vcf_parse1 by skipping fields which are not needed.
adds d98a119 do not round per-sample average depths to integer values
adds a8e4773 Merge pull request #8 from sm15/develop
adds cc0285e Merge branch 'master' of github.com:samtools/htslib
adds 5963c16 Updated test file for vcfcheck
adds d191f5e vcfnorm fix: segfault on nasty case of indel; synced_reader fix: read from stdin
adds 5d91d67 vcfnorm: Sanity check for reference sequence mismatches
adds 7e47a55 vcfnorm: Bugfixes, more robust realignment, more sanity checks.
adds baaee35 merge r199 changes; part 1
adds cb0c9af merge r199 changes; part 2
adds c0c76dd merge r199 changes; part 3
adds 317adce added bam2bed
adds 7ec0534 r198: tag version
adds ea42b99 r199: reduce one conflict when merged with master
adds 69cf929 r200: the previous is not good enough
adds 7581e65 Exported some routines
adds b57e308 Allow to skip errors
adds eaa78d2 Append new header lines
adds b6ebfdb added this missing file
adds 078817b Merge branch 'lite'
adds cd6a15d bam2fq: skip secondary alignments
adds 168452f Merge branch 'lite'
adds 3fcccf2 Bugfix: core is a member of bam1_t->core
adds 5e9cebd Merge pull request #9 from kmsquire/fix_secondary_check
adds d9ae9b4 Merge branch 'master' of github.com:samtools/htslib
adds 0831df4 vcf_format1: move the string initialization outside so that the method can work in append mode (used by vcfquery)
adds 3c309c8 synced_reader: Allow reading of unindexed .vcf and .vcf.gz in more situations
adds 1f9cd24 vcfquery: Do not crash when no arguments given
adds 0d29f5d vcf.[hc]: convenience routine for converting BCF_INT types into C ints
adds d64ba91 vcfgtcheck: new functionality - multi-sample cross-check of genotypes
adds 996f0de bcf_set_iarray: fix in incrementing typed pointer
adds 7f5b3e6 gtcheck: added per-sample depth plot
adds aecef4d vcfgtcheck: Slight change in semantics, -g now used only for the known genotypes.
adds 5cba9d8 bcf core lib: PASS filter must come first in order to conform to BCF specification
adds 851df67 bcf core lib: Fixed a silly bug from the last commit. FILTER=PASS indeed must come first, but only after the ##fileformat string.
adds b89ba2f compiling error
adds ebcc4be optionally output OQ instead of QUAL
adds 1c631e9 Merge branch 'lite'
adds 7e67a39 Listed copyright and license notices.
adds ef70ad5 Draft package.
adds 6d906ba core vcf: added API for modifying/deleting/adding INFO fields, currently only VCF output supported; vcfmerge: AN,AC tags now updated correctly.
adds 5b0880e vcfcheck: Do not crash at non-variant sites. Restore checking of two VCFs.
adds baa5708 VCF/BCF core lib: Allow missing values in vectors. Note that this is a major change which, in contrast to BCFv2.1 specification, allows missing values in vectors. For integer types, the values 0x80, 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, 0x80000001 as end-of-vector indicators. Similarly for floats, the value of 0x7F800001 is interpreted as a missing value and 0x7F800002 as an end-of-vector indicator. This trial BCF version (v2.2) is c [...]
adds eef8320 gtcheck: Removed forgotten debugging line
adds 73f147b A few bugfixes from the previous two commits. New -S option in gtcheck and -H made work also in the cross-check mode
adds 2f5843a vcfquery fix: Allow a mask file with the -v option
adds d09058b vcfcheck: complain if tabix index not available with -t option
adds 7141bd5 vcfcheck: Do not run in streaming mode with the -t option
adds 4cf9350 vcffilter: fixed a typo, output file names now named correcly based on filter type
adds 84901c3 bcf1_update_info fix: initialize bcf_info_t pointer, do not pass NULL
adds d01fcee vcffilter: extended help message
adds 19ca371 vcffilter: allow arbitrary order in -f and -l filtering options (X>value is same as value<X)
adds b1c5fea vcffilter: plot annotation distributions
adds eaee02d vcfview: Restored the subset functionality
adds aae973b vcfview: Restored the subset functionality (continued)
adds 1ed4f54 vcfmerge: do not crash with non-overlapping chromosomes
adds 54868e8 vcffilter: Plot also cropped annotation distributions to show the range of values actually used in filtering
adds 35ed1b5 vcfgtcheck: Fix in INFO/DP parsing, wrong ID was used before
adds 944c4b0 vcfmerge: fix of copy-and-paste error in format field merging, use correct integer ranges
adds 89f7e5d gtcheck: fixed incorrect output, instead of uncertainty, the opposite (confidence) was reported before
adds 7d76f62 vcffilter: check to prevent division by zero in the python plot script
adds 1dbfae8 vcfisec: in the sites output mode print also file mask
adds f4bfe4a vcfquery: Enable -p option again
adds 6a5a672 vcffilter: Plot also bad sites in annotation distributions. Updated test files.
adds 5d717a2 vcfmerge, vcfisec: Change in synced reader's API, allow unlimited number of input files. (Previously the limit was sizeof(int)*8)
adds 974d20b Fix crash on legacy files
adds 46a4b6a Use sizeof() and NULL instead of numbers
adds ce6022e Import header comments from samtools
adds 99b8b89 Add const to char *'s to ensure they can be called with fixed values without triggering compiler warnings
adds f6c95a1 Merge remote branch 'mp15/develop' into develop
adds 429216a vcffilter: backup commit, bad SOM now working
adds 12b827f vcfcheck: Fixed a bug introduced by recent changed in synced reader
adds 5b49a22 vcf core lib: Added sanity check to catch up common problem makers, such as PL declared as Number=. instead of Number=G; Support for output of more than 64 alternate alleles; API to access bcfinfo_t header line information.
adds fb0d88d vcfmerge: Fixed subtle bugs revealed when merging FMT fields of different lengths; Append version string and command to the output VCF header
adds 222fe6c vcffilter: First step towards indel filtering - new switch to select from good sites mask
adds f344f7a vcffilter: skip the two additional score fields when applying SOM filters
adds 8e14b56 vcfcheck: create additional ts/tv stats which counts 1st alternate allele only
adds f15f7bc vcfcheck: More readable output, replace "-" by "<STDIN>" when reading from standard input
adds b281180 vcfview: Fix in bcf_subset; force unpacking on VCF output
adds e91d10b tbx: Allow indexing of empty files, do not segfault
adds db1edf3 vcfutils: bcf_gt_type should not be declared as static
adds 5da7aef vcf.[hc]: API to update FILTER column. BCF output not supported yet in this version
adds 49f9e95 vcfmerge, vcfnorm: Append command and version string to VCF header
adds 3164242 vcffilter &friends: Filtering of indels now supported. Changes in vcfcheck, plot-vcfcheck and vcfquery to reflect that. More changes and fixes to come, but this version seems stable and fully functional.
adds 3f76a40 Updated tests
adds 72b5b28 vcfcheck: Changed output format of Ts/Tv
adds 45be6fe vcffilter,gtcheck: Added sanity checks; Extended help message; Changed the order of columns on gtcheck output
adds 4523040 plot-vcfcheck: Produce the overlap by AF graphs
adds fdcfa2f synced read and vcftools: Changed the -f, --apply-filters switch so that it accepts a list of allowed FILTERs. This is useful for example in cases when PASS has to be distinguished from "."
adds a634ce9 vcffilter: FILTER column of hard-filtered sites now lists failed filters; Unset the FILTER of skipped sites only with -u switch, not by default.
adds efa9530 vcfcheck: Fixed a bug in initialization of frame-shift calculation; More detailed FS output
adds 7a5992c vcfnorm: Removed two assertions to allow realignment of MNPs
adds c3d530e vcffilter: Change in neighbourhood function in SOM training, seems more robust with respect to random seed
adds c9873a3 correct typos
adds a7f24e2 deal with Number=A and Number=G INFO and FORMAT fields when trimming alleles
adds a7f4597 add new tool vcfsubset
adds c420b54 add tests for vcfsubset
adds d30f1aa resolved test/check.chk conflict
adds 1994af5 vcfsubset: New -i,-e options for general filter expressions. In this version, only QUAL and INFO columns are supported.
adds e47feba vcf core lib, vcfsubset, vcfmerge: First step towards binary BCF output. Functional but probably buggy.
adds c3622b8 Revert to kstring.h with a separate kstring.c
adds a458ed8 Fix <stdarg.h> include
adds ac479c3 Merge changes from samtools's kstring
adds 8876289 Replace with samtools's ksort
adds e567ef0 Add klist.h, as used by samtools
adds 0c275f6 Maintain the same API regardless of -D BGZF_MT
adds b267fb4 Expose bam_hdr_init() in the public API header
adds 8496905 Avoid conflicting with samtools's bam_index()
adds 0670753 Merge branch 'for-samtools' into develop
adds 8b095aa Port fixes from samtools razf.c/h to htslib.
adds eedca8d Merge branch 'razf_sync' of https://github.com/mp15/htslib into develop
adds 0fb04c2 Add Travis CI control file
adds 348c5a1 Merge branch 'master' into develop
adds dbcc082 Resolved vcfmerge.c merge conflict
adds 3ecd0cb vcfsubset: Make --apply-filters consistent with other tools
adds 779e243 Merge remote branch 'remotes/sm15-mod/develop' into develop
adds 3c4259c vcfcheck: re-enabled stats by QUAL
adds bdb550f Move format specifications to sam-spec repository
adds cbc4478 Test with both Clang and GCC
adds 7508806 Merge branch 'develop' of github.com:samtools/htslib into develop
adds 7413bed Deleted files which were moved to the new samtools/bcftools.git repository
adds ad5ee37 Remaining application code also moving repository
adds dd9c5a2 Lift library source to the top-level directory
adds f455afd New non-recursive build infrastructure
adds 6799348 Build shared libraries, add "make install" target
adds 9ec7860 New API for BGZF indexing w.r.t uncompressed data. Extended BGZF to read uncompressed files. Moved from RAZF to BGZF in FAI indexing.
adds 956f45b bgzf.c: Check return status of bgzf_read_block in bgzf_useek to catch gzipped (as opposed to bgzipped) files.
adds 6af2c1d [hts_open,bgzf,vcf] New flags for uncompressed input/output to distinguish between compressed/uncompressed BCF/VCF. Updates and fixes in BCF update functions. Removed old tests (now in samtools/bcftools repo) and added new.
adds 039620b Update khash.h from upstream sources
adds 6d9e20e Update kstring.[ch] from upstream sources
adds ab92989 Bug fix to handle blank headers in SAM files
adds 4b8c9b5 Bug fix to stop sam view from converting 'H' into 'Z' types.
adds 83a9bdd Use strtoul instead of strtol for XX:B:I tags so that integers >2.14 billion work.
adds 8256ea8 Use strtoul() for other unsigned 'B' types too
adds fcb9563 constify input parameter to faidx_fetch_seq
adds 750f564 Use config.h for configuration options
adds c2e9391 Replace HTS_VERSION with hts_version()
adds 842b21c Actually $(NUMERIC_VERSION) is more generic
adds c485827 Resolved merge conflict in Makefile, merged.
adds fb60f0c vcf.h: Reverted back to bcf_float_is_* macros as the inlined unions break vcfmerge code, found a solution with the original version.
adds f59d50f vcf.h: New bcf_get_info_* and bcf_get_format_* calls
adds 9946dc7 Fix union-based type-punning buglet
adds 1f9b3db Use static inline, not just inline
adds 919fd54 Keep the makefile non-recursive
adds 12c677b Add faidx (FASTA index) description man page
adds b68bfbf Merge branch 'develop' of github.com:samtools/htslib into develop
adds 818a5ed hts_open,bgzf_open: Changed semantics of the "u" flag. Originally "u" was equivalent to "0", which on output yielded uncompressed data in the zlib format. Newly "u" results in plain uncompressed output.
adds aac4601 Alphabetise, fix whitespace [minor]
adds 8e00f34 Merge branch 'develop' of github.com:samtools/htslib into develop
adds 14a22ef vcf: Make sure GT comes always first in bcf1_update_format; Do not loose last newline in vcf_hdr_read; Updated tests.
adds 55d6f39 vcf: Changed semantics of bcf_get_[info|format]*() ndst parameter: interpret as number of elements in the array, not the size in bytes. Allow overlapping memory blocks in bcf1_update_alleles
adds 1013c35 synced_reader,vcf: Big rewrite of synced reader to allow more flexible handling of regions and targets in future.
adds ff1465e This commit fixes issues in hts_open and bgzf with uncompressed BCF input, BGZF now detects uncompressed streams on the fly. Fixes in FILTER and FMT part of bcf1_sync.
adds cb5cacc kfunc: Moved the kt_fisher_exact test from the original bcftools into htslib
adds fd086ed bgzf: Fixed typo in block_address calculation in bgzf_seek
adds 60f315f synced_vcf_reader: new bcf_sr_get_line macro and fix in vcf/bcf index interator initialization
adds a6e1c9f vcf: Minor bug fixes and API touches
adds d49e3f6 kseq,hts: Enable seek() on kstreams and hts_useek(),hts_utell() on htsFiles. New module which allows sweeping BCF/VCF files both fwds and bwds
adds a3dae45 vcf: prevent segfault when sample columns do not exist but FORMAT column does
adds 85ecdc2 Add buffered low-level input/output streams
adds 70b088e Warn if hFILE function return statuses are ignored
adds 009dfb7 Refactoring [minor]
adds 2b9a9d2 Add hseek() and htell() test cases
adds 99f05d3 Flush or discard the buffer in hseek()
adds 441af2e Maintain our own hFILE offset within the stream
adds 1a7dae0 Add hdestroy_buffer() for use in hopen_*() cleaning up
adds 3c3d80a BGZF worker threads do no I/O themselves
adds f20bae1 Use hFILE underneath BGZF, and add bgzf_hopen()
adds 655227b Add hfile*.[ch] to $(HTSLIB_ALL)
adds c88645c Merge branch 'io' into develop
adds 5750966 Fix vcf_sweep.h dependencies
adds c371324 Also run our tests
adds 5bbaed6 Fix typo [minor]
adds 3fa19a7 Lift mallocing & freeing to the generic hFILE code
adds 25459e9 Merge branch 'develop' of github.com:samtools/htslib into develop
adds 78bb557 On Windows, call knet_win32_init before using knet
adds 5a5fe13 Merge branch 'develop' of github.com:samtools/htslib into develop
adds 5e277dd synced_reader: Expanded docs - example of usage
adds 799ed4a vcf: Support for string values in FORMAT; handling missing BCF_BT_CHAR values in bcf_fmt_array()
adds c9734f7 VCF header parsing: Handle pathological cases where less-than and greater-than signs are used in place of double quotes
adds aca31de vcf: Non-critical vcf_parse1() errors must not go unnoticed by vcf_write1(). Fixed offending \0\n added by bcf_hdr_subset()
adds fd13d8c Fixes in targets/regions VCF synced reading, now regions work when streamed. Removed redundant get_fmt API calls
adds 4352ff1 Minor docs comment added
adds 193ac2f Fix -Wc++-compat warning / C++ compilation error
adds c0a0035 Remove unneeded cast
adds 4be3a31 Don't #include bgzf.h from other htslib headers
adds e7a2de6 Change *_itr_next() to take htsFile*, not BGZF*
adds 663f12e Replace "void *fp" by a union of the file pointers
adds 29290bc Use hFILE instead of stdio for uncompressed output
adds ac7844a Add bgzf_raw_read() and bgzf_raw_write()
adds 9dfcc35 Merge branch 'io' into develop
adds 1de141b Merge branch 'develop' of github.com:samtools/htslib into develop
adds 5ec2456 bgzf: Added ad-hoc checks to all hfile calls to keep compiler happy
adds b0312f8 bcf_index_build: Check return status of helper calls
adds d5bd42c Properly ignore hclose() in bgzf_[d]open functions
adds 67a9231 Merge branch 'develop' of github.com:samtools/htslib into develop
adds bbd6647 synced_reader: Added support for alleles in targets files to select best matching line out of possibly duplicate VCF records.
adds de484cc vcf: Added bcf_get_variant_type[s]() call to avoid the need for explicit call of bcf_set_variant_types(); The mpileup's X allele is not a SNP; Get rid of htfile warnings
adds 7b85b13 Proper initialization in hts_readlines
adds 2ea61c2 bcf_index_build: Check if the BCF is compressed
adds c6a1c65 Fixed a rather surprising bug in CSI index access via hts_itr_next, before it was not possible to obtain BCF record at chr:pos-pos. The fix may have unexpected consequences in other situations and file formats, beware!
adds bce13c4 vcf.c: Proper freeing of memory taken by dirty info/fmt tags when update routine called multiple times
adds 59c317e New feature in bcf_synced_reader: negate the sample selection in bcf_sr_set_samples by exclamation mark
adds a4736dc vcf.h: Add out of range check into bcf_idinfo_exists() as it always has to be checked elsewhere.
adds 9f6f905 vcf.h: New API call: bcf_get_genotypes()
adds 07d5457 vcf.c: Call bcf_unpack() on user's behalf in all bcf1_get/update routines
adds 35621c0 synced_reader: Fixed an off by one error in bcf_sr_next_line() to properly match target alleles
adds 3f4ecdf vcf: Tidied up vcf.h, made API more consistent and extended documentation
adds bc86c10 vcf module: Made the naming more consistent to avoid confusion about which of the vcf/bcf_* function variant to use.
adds 95321be Merge branch 'bcftools+calling' into develop
adds 616a0a5 Enable warnings only if -Wno-unused-result works
adds 518619b Added CRAM support to htslib and htscmd samview. This is just a port over from the samtools io_lib subdirectory and has all the same nasties and duplication of abstract data types.
adds 2424c14 Merged with attractivechaos/klib: - add upstream kvsprintf and rework ksprintf - add upstream printf attribute checks - use our kputw (has MIN_INT bug fix) - keep our extra functions (kputc_, kputsn_, kputl)
adds e79e112 Major overhaul of CRAM code (originally imported from Samtools/htlib branch, and further back from Staden Package io_lib).
adds 6df8103 Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds 47b7241 Further removal of various unusued portions of Staden io_lib.
adds 417fc59 Switch from modifying CFLAGS to CPPFLAGS so we can do "make CFLAGS=-g".
adds fa5d1a1 Bug fix to handle blank headers in SAM files.
adds 5500ef0 Bug fix to stop sam view from converting 'H' into 'Z' types.
adds 016efd5 Use strtoul instead of strtol for XX:B:I tags so that integers >2.14 billion work.
adds e25066b Better handling of unknown references.
adds 0649ecb Bug fix to khash-ification of sam_hdr_add_lines
adds 7012805 A bit of a hack to set the header and references up properly for cram. This is a hack right now as it requires accessing internals of the fp, but it should be fixed in future by properly supporting methods to manipulate these fields for all data types rather than just cram (eg see scram.c in io_lib).
adds 1e6f3cf Added some synthetic SAM test data and a test perl script to trial conversion between SAM, BAM and CRAM. A work in progress.
adds eeb41a7 Bug fix to khashification of process_one_read.
adds 13698ea Added tests/test_view
adds f716f35 (io_lib r3438/7)
adds 525c5bd (io_lib r3439)
adds 70a227b (io_lib r3460)
adds 95d7e53 (io_lib r3461 minus arithmetic coder & last_name experimental parts)
adds 8a76b46 (io_lib r3467)
adds 265e2e7 Silenced a "pointer targets in initialization differ in signedness" warning.
adds b3dccc2 Merge branch develop of github.com/jkbonfield/htslib into cram
adds c41394f Move cram/ directory to the top-level
adds 159a498 Add makefile dependencies for cram code
adds 7fe5680 Merge the CRAM test harness into current htslib
adds fb94dac Build test_view with -pthread
adds 30cf9e9 (io_lib r3470) Fixed re-calling refs2id so it clears cached r->last; the pointer becomes invalid.
adds 26425fa Merge branch 'cram' into develop
adds e806853 Remove -Wc++-compat for the sake of the CRAM code
adds 037860b Add bam_endpos(const bam1_t *)
adds aa50834 Disentangle CRAM header loopiness [minor]
adds 23d64b8 Merge branch 'develop' of github.com:samtools/htslib into develop
adds 43e8305 hfile: Removed accidently commited local change in blksize
adds 1ee29f4 Add SAM and VCF man pages extracted from samtools.1
adds 1c9239f Add BAM_FSUPPLEMENTARY flag bit
adds 638083f Get rid of %ld compilaiton warnings
adds cf02167 Return bytes >= 0x80 from hgetc() correctly
adds d359060 Fixed CRAM to code with the 0x800 supplementary flag.
adds 4294c7f Merge pull request #27 from jkbonfield/develop
adds 10ef097 vcf: New bcf_hdr_printf() call
adds ab5077b Merge branch 'bcftools+calling' into develop
adds a1e76ad vcf: Print a comprehensible error message if unsupported version of BCF is encountered
adds dc77561 Move cram_seek() from cram_index.c to cram_io.c
adds 6416ebf Use hFILE underneath cram_fd, and add cram_dopen()
adds 3b9ba8e hts_open(fname, "r") detects format by peeking at the input
adds b02146d Merge branch 'io' into develop
adds b92504a Tab, newline, etc are not control characters
adds 65a3ed4 Require lowercase [rw] mode letters in bgzf_open() etc
adds ba4e3fc Limit input hFILE buffers to 32K [temporary hack version]
adds 1282758 Fix tbx_itr_next() when given a textual (is_kstream) htsFile
adds 091f27e test.pl: fail if any tests fail
adds d37f6df hts_open(fname, "r") now works in both cases; no need for "rb"
adds 44fc956 Format detection: non-compressed binaries; is_compressed setting
adds 7eb91ef bcf_sr_open_reader(): Auto-detect input file format
adds 43586c9 The file type not necessary any more when opening synced reader
adds c413e8a Merge branch 'develop' into bcftools+calling
adds e2e0a4b Reverted a fix of "chr:pos-pos" index queries, the original version now works.
adds 18f6183 Handle erroneous modes with neither 'r' nor 'w'
adds b5f5f16 Added copyright notices.
adds d3803f3 Fixed errors in copyright due to pasting the MRC one and forgetting to change the organisation name. Oops!
adds 116ccd2 Fixed a variety of multi-threading data races, detected through 1000 repeated runs of the same command at approximately the 2% failure level on unsorted data only.
adds d80899b Merge CRAM copyright notices and data race fixes from jkbonfield
adds c83a9c0 Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds 808b36f Samtools. The test harness worked, but the samtools interface needed an additional cram_set_header function as we don't pass this over when opening the new cram file. (Try#2 - previous commit accidentally rolled back an upstream change from 2 hours before.)
adds f149e78 Added prototype for cram_set_header()
adds bebdfea Merge cram_set_header() from github.com/jkbonfield/htslib
adds c7612be Fixed a couple complaints from clang.
adds b185d95 Fixed a bunch of code warnings produced by clang's static analyser.
adds b3d93ad A couple more clang reported errors, which are duplicates of previous ones. I assume omitted before due to duplication.
adds a3fd2b0 Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds 6fd937f Robustness improvements following fuzz testing. (See io_lib r3500).
adds 941b400 Merge branch develop of github.com/jkbonfield/htslib
adds 2402fc0 Add hts_set_fai_filename(); parse .fai in sam_hdr_read()
adds 2591937 Remove now-unused fn_aux hts_open() parameter
adds f010407 Reinstate distinct bgzf_check_EOF() status for seek failure
adds d1f589d bcf_gt_type can now, optionally, give the index of the 2nd alt allele for GT_HET_AA genotypes
adds c16f20b Merge pull request #33 from sm15/develop
adds e5b2ce0 Merge branch 'develop' into debian/unstable
adds a9d9405 Documented cram/*, collated copyright notices for works under the MIT license.
adds 2fc6f3b Do not build a htslib binary package: there is not htscmd program anymore.
adds c861097 Install in and from debian/tmp.
adds ff10faf Add hclose_abruptly() for stack unwinding after errors
adds d038d8e Change hts_close() to return int (error indication)
adds 69778ad Fix bgzf_write() for large (> 2GB) blocks
adds f981604 Merge branch 'develop' into debian/unstable
adds d131c15 Corrected paths.
adds bd6afa8 Make the package multi-architecture.
adds 64a155a Align package name on soname.
adds 708a9cf Clean test directory before packaging it.
adds 99fb99a Submitted ITP #729282 with the current package descriptions.
adds 1f0dec9 Align package name on soname.
adds f823fee Merge branch 'debian/unstable' of github.com:Debian/htslib into debian/unstable
adds e6a750b Uses pristine-tar and may use git-buildpackage.
adds 802bf74 Upstream tag 0.2.0_rc3.
adds e870f95 Watch GitHub.
adds 937513b Mangle the upstream name, so that the tarball has a correct version number.
adds 2f7c559 Empty symbols file, to be populated by Debhelper.
adds 129889c fakeroot dh_makeshlibs | patch -p0
adds 8f1d57c Removed minor number.
adds 3a74341 Corrected length of lines.
adds 7ffdf2a Make dh-exec files executables, since we are using the 1.0 source format.
adds 0b49d2f Pass dpkg build flags.
adds 07a47f6 Make libhts-dev depend on libhts0.
adds 1f97dc0 Prospective VCS URLs (Alioth is currently down…).
adds 00c7f03 htslib (0.2.0~rc3-1) unstable; urgency=low
adds 420896b Override PACKAGE_VERSION to avoid tags with a slash in the name.
adds 72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode.
adds 6561746 Compile cleanly without warnings with gcc 4.6.3
adds 2b7806d Fixed return status checks of fread calls
adds f1d9f6f Merge branch 'develop' into bcftools+calling
adds 69cf8a2 vcf: Support for regions in the form chr|chr:pos|chr:from-to|chr:from-
adds 9cef38d tbx: Sanity check if the file type meets the expectation, detect non-numeric fields
adds 65450dd hts_idx: check return status of bgzf_read
adds 19beee0 bcf reader: Fix in chr:pos type of regions
adds 5b22605 synced reader: Support for BED regions/target files
adds ae0de02 synced reader: regions and targets now support VCF; Fix for match_alleles by reverting 0-terminating chr modification
adds 66c4f41 synced reader: Give a hint when tabix was used with wrong column indexes for regions/targets
adds a8bc3b1 pileup: Detect non-recoverable errors and exit with proper status
adds 223459a vcf: new APIs bcf_alleles2gt and bcf_gt2alleles; bcf_synced_reader: recognise compressed BED files
adds 20b8bf5 Resolved merge conflicts
adds 7994a4b Merge branch 'bcftools+calling' into develop
adds ba56a71 Merge branch 'develop' into debian/unstable
adds 96badc4 Changelog for work in progress.
adds 7a66c32 Updated symbols file.
adds 1b2bc6e Added decoding checks for the most obvious of sam parsing failures.
adds 3f3758d Removed old comment from earlier code.
adds 3e18c41 Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds bef7597 Further fixing of auxiliary tag decoding.
adds 1344221 Added the ability to do samtools index on a CRAM file.
adds bc53b5d Merge cram_index_build() from github.com/jkbonfield/htslib
adds 923191c l_qname is unsigned, so is always >= 0
adds bb71572 Ensure r is clearly always initialised [minor]
adds 4e4501c Use $(LDFLAGS) & $(LDLIBS) when linking shared objects
adds d6e1ad0 Use the exact type in malloc(N * sizeof(TYPE*)) etc
adds 13b445b Fix pointer arithmetic [minor]
adds 06eeee1 Add HTS_NORETURN and annotate fail() as such
adds be359b5 Merge remote-tracking branch 'upstream/develop' into debian/unstable
adds 86fd29c Refreshed changelog after pulling new upstream tag.
adds f3bd296 New upstream tag; no new copyright nor license statement.
adds d870946 Adjusted substitution variables following dpkg's warnings.
adds 79b5d4e Use the Debian as package version.
adds b60c181 Updated the changelog.
adds 9469458 Removed debug command accidentally introduced.
adds 6f5473a Merge branch 'develop' into bcftools+calling
adds 715f5db bcf_remove_alleles: Assume diploid genotypes if the ploidy cannot be determined, better to proceed than crash.
adds 18a5382 vcf: Update rlen on BCF output, this is important in BCF indexing, rlen is used as it is. Todo: also END should be checked with symbolic alleles
adds c8ec7cb Merge branch 'bcftools+calling' into develop
adds 7b2a2d0 Merge branch 'develop' into debian/unstable
adds 626a888 Use the exact type in realloc(N * sizeof(TYPE*))
adds ea407fe Merge branch 'develop' into bcftools+calling
adds cf12fba sam: New bam_str2flag and bam_flag2str functions for a more user-friendly setting of bitmasks. Removed the default pileup filters (except for BAM_FUNMAP) and moved the filtering to BAM-reading callbacks
adds 5d68967 Merge branch 'bcftools+calling' into develop
adds 5d609bc Merge branch 'develop' into bcftools+calling
adds 7092725 Merge branch 'bcftools+calling' into develop
adds 1a76ced Merge branch 'develop' into debian/unstable
adds 648c826 New upstream tag; updated changelog.
adds fa1a13a Updated Symbols file.
adds d49f20e faidx: Detect compressed BGZF fasta files and create .gzi index without asking to allow proper functioning of samtools faidx fasta.fa.gz
adds 0908d4c synced_reader: Improved regions/targets to be faster with large number of sequences; More userfriendly regions_overlap() function
adds 5e770b3 vcf: bcf_update_format now sets the number of samples in VCF record which previously was responsibility of the user; Fix in bcf_itr_querys macro, non-existent bcf_name2id renamed to bcf_hdr_name2id
adds 32187cc Merge branch 'develop' into debian/unstable
adds 53af783 Updated symbols again.
adds f192318 vcf: Support for IDX BCF tag
adds 0c084f2 vcf: Output . for missing INFO, FMT and samples
adds 9029156 vcf.c: Fixed a renaming artifact, bcf_clear1 should be bcf_clear
adds 9d6defa vcf: qual now set to missing on bcf_clear; Avoid warnings about type-punned pointers
adds 997c519 Output VCFv4.2 header
adds ebd9b94 Cope with empty containers internal to a CRAM stream. Technically empty containers shouldn't exist as the specification states they must contain at least one block. However this is a useful precursor to the EOF block checking.
adds 3e96dd7 Added implementation of cram_external_encode(). It's not yet used except in experimental versions, but opens up the route to storing more CORE data in external blocks to make partial decoding simpler (eg CRAM->FASTA).
adds 70efcd9 Bug fix to the zlib strategy tuning in multi-threaded mode. It could (legitimately) drive the number of trials negative, but this meant it never left the trial phase and consequentially encoding speed more or less halved the instant we asked for more than one encoding thread.
adds a935e3c Added refs_t->last_id (note distinct from ->last) for use when reading from MD5 server. This reduces excessive reloading of the file in certain cases.
adds 1a39edb Add mfsteal to mFILE, and use it in cram_populate_ref.
adds 34227f8 Added missing return code checks. Fixed 'x' mode of mfreopen.
adds b5ccf9b Merge branch 'develop' into bcftools+calling
adds 06208f2 Updated test
adds ea4dbc6 add support for Number=R fields when trimming alleles
adds cfdc6fd vcf: Make sure fileformat is added only once
adds 78a6ef3 Merge branch 'develop' of git://github.com/samtools/htslib into feature/number_R
adds 312add9 vcf: New bcf_get_info_string() wrapper
adds f78d671 vcf: New API bcf_get_format_string()
adds 2b801d7 add support for Number=R fields when trimming alleles
adds 0caf597 Allow overriding default columns indexes in bcf_sr_regions_init
adds c7c3ada vcf: new function bcf_remove_filter()
adds 36a8ce9 Merge branch 'develop' into bcftools+calling
adds 03f3fd7 Merge branch 'bcftools+calling' into develop
adds 4855f43 vcf: fix in bcf_get_genotypes, sanity check too strict for GT
adds b57379f vcf: Tip to workaround missing contig tags
adds b2aab8b hts indexing: Allow arbitrary chromosomal order.
adds 2d0423a vcf: New bcf_hdr_id2hrec() and bcf_hrec_format() functions
adds 96132f4 vcf: New vcf_write_line() function
adds 600acc3 synced_bcf_reader: New bcf_sr_seek() function
adds e7ffc82 vcf: New bcf_translate() and bcf_hdr_combine() API
adds 60c22d4 idx: Support for "." queries to retrieve all records
adds 4622eaf vcf: New bcf_has_filter() API function
adds 9dbf592 Fix hseek() return value test
adds 2daf614 Make filename argument a *const* char pointer
adds 650202c Strict matching of strings in bam_str2flag
adds b729954 vcf: new experimental bcf_hdr_set_samples() for subsetting
adds 0eb4c88 Merge branch 'bcftools+calling' into develop
adds 68848e2 bcf_hdr_set_samples() recognise lists vs file names
adds fd657c4 Store readrec function pointer within hts_itr_t
adds a60ff3f Make search key arguments *const* char pointers
adds a8be0b8 Write strcmp() comparisons comprehensibly
adds f0fb825 Add basic test exercising bcf_itr_queryi and bcf_itr_querys
adds 4d123f2 hts_itr_querys() calls hts_itr_query() via a function parameter
adds 655edab Add sam_itr_*() dealing with BAM and CRAM iterators interchangeably
adds 42152a6 synced_reader: Better handling of target alleles
adds ad17bb8 bcf_sr_set_samples to use the new --sample convention
adds fde4bd9 vcf: New bcf_get_info_flag() API
adds a6cbed2 Added some EOF block creation and checking.
adds ae92627 Bug fix to cram_next_slice(). The new while loop checking for non-empty blocks caused a crash when multi-threading.
adds 3a4aac5 Bug fix to EOF block writing when in multi-threaded mode (not yet supported in htslib's cram interface). It was writing the EOF block before flushing any pending threads.
adds dc4d0f1 Added a check to EOF in Cram in hts_close(). Note that this isn't the same place that BAM checks as it does it in hts_open(), however the benefit of doing on close is that this check can work when inputting from a pipe.
adds edb12c3 Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds 76cfc12 Updated the Cram EOF block detection to avoid falsely considering the lack of an EOF block as an error when doing a sub-range query.
adds 939f6ea Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds 19ccc09 Fixed initialisation of CRAM indexing when the CRAM file contains refids that aren't sequential.
adds c68d523 Initialise beg and end values in the hts iterator. Without these mpileup simply bails out after fetching the first column as end is 0.
adds 843a063 Fixed the iterator to be 1-based inclusive coordinates for CRAM.
adds 025ecb3 Also initialise tid in case user code looks at it
adds 0e76a59 Merge pull request #46, CRAM EOF blocks
adds bae6c41 vcf: Abort on broken VCFs with multiple/trailing spaces/tabs
adds 0038f9e vcf: Don't let unpack_*_core forget the to-be-freed pointer
adds c62982e hts_expand0: type ptr properly, it can be of different type
adds b932f95 The default CRAM version is now 2.1. This is now the official release for supporting EOF blocks and the Java implementation only enforces them for CRAM 2.1 and above.
adds 322b28b Fixed EOF check. The usual code path had the correct check, but an empty cram triggered the incorrect code.
adds dc45cfc Bug fix to the SAM header padding. It could go negative and then fail to write the header.
adds 2279b3e Merge pull request #60, CRAM EOF block improvements
adds 85b864f To avoid confusion, make bcf_get_*_int and bcf_update_*_int symetric
adds aac5df5 hts_idx_load: Print warning when index is older than data
adds 5e03160 Make synced reader aware of bcf_hdr_set_sample(), expanded docs
adds 2eb509e Reduced the number of realloc calls zlib_mem_inflate(), while hopefully not overallocating much either.
adds 728ad50 Merge pull request #62, minor CRAM updates
adds d4d37c0 synced_reader: New bcf_sr_region_done macro
adds 5a340a1 Check cram_eof() before calling cram_close()
adds 39558ce bcf_translate: Catch unchecked errors
adds c336894 More sensible Quals of matching bases in overlaps
adds bcbfe37 Ignore operation-not-supported errors in fd_flush
adds c38cf60 Keep the style of the surrounding code
adds bdb6a4a Add HTS_IDX_NONE and document HTS_IDX_*
adds f6c37a5 Fixes incorrect MD5 calculation in cram_write_SAM_hdr
adds 21ca653 Merge #68, fix incorrect length given to MD5 calculation
adds 3ea22a1 Add 'a' (append) mode letter; propagate mode letters
adds 0d95c21 Add "data:blahblah" in-memory hFILE backend (read-only)
adds cb7f6e9 fix remote fetching of regions for bam and vcf
adds babaaf3 Use hFILE rather than knet in test_and_fetch()
adds 1069b17 Merge #70, fetching of remote BAM/VCF indices
adds 78e237b Fixed a bug when loading in fasta files consisting of all sequence on a single line and in lowercase.
adds 5c65920 vcf: Allow omitted trailing FORMAT fields
adds 692bb41 Fix sam_format1 failure on lines ending in integer/float tags and issue #63
adds 30b4033 Rewrite __skip_tag() as skip_aux()
adds ab84296 Add sam aux field tests
adds 20df6b9 Merge sam_format1() and __skip_tag() fixes (PR #73)
adds 5bdc06d synced_reader: Init position correctly
adds c6f8531 Add ks_release() to kstring.h
adds 321c402 Reinstate bam_header_dup as bam_hdr_dup
adds fb23174 Fix typo in comment
adds fee84e0 synced_reader: Init position correctly
adds fca50b8 Merge branch 'develop' into bcftools+calling
adds 1435a5d Merge branch 'develop' into bcftools+calling
adds d91c9bb Merge branch 'bcftools+calling' into develop
adds fe173b6 Make hfile.h part of the public API
adds d7f0ae1 Add MIT/Expat license boilerplate
adds 0180921 Define __attribute__ macros in a new (semi-public) header
adds ec3a15a Fixed comment typo
adds 22dedbe Merge pull request #79 from spalte/comment_typo
adds cc207d8 hts_idx: fixed indexing of NO_COOR blocks
adds cf693ad This resolves #49
adds d66571e Propagate error codes for CRAM_OPT_RANGE
adds 3490604 vcf: Propagate error in bcf_hdr_append
adds 9d640ff Fixed off-by-one in bcf_get_format_values
adds 9dec00e Construct HTS_IDX_REST and HTS_IDX_NONE iterators without an index
adds b26a445 Propagate error from bcf_hdr_printf
adds f7953db hts_readlist modifed to explicitly indicate file name vs list
adds acfeb8a make sure we have found values for AC _and_ AN before using
adds 5c80322 Merge pull request #82 from sm15/feature/bcf_calc_ac_bugfix
adds 503c95a Support for =X cigars in mpileup overlaps.
adds bb4721c faidx: Set error status if unknown seq is queried
adds cd410e1 Add duplication function for the bam1_t interface
adds 42d6aa1 Merge bam_dup1() addition (PR #80)
adds 3e52ddb Migrate documentation from samtools bam.h to sam.h and add a few more items
adds 128d97d bcf_hdr_subset: To allow sanity checks, mark missing samples
adds 52ecc97 bcf_sr_seek to seek to start with seq=NULL
adds eed28cb bcf_remove_alleles: Fix indexing range for Number=A alleles
adds df2c538 Silence -Wstrict-prototypes warnings
adds 388abc7 Fixed BCF output after bcf1_sync_alleles, simplified
adds 4a5dcf4 bcf_remove_alleles to work with BCF output
adds f5c96ca Added bgzip and tabix
adds bd6ed8b .gitignore tabix and bgzip
adds 20b6f6d Create trunk copy
adds 8b14e7f Change copyright notices now that MIT has approved open source distribution.
adds 4c42d43 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
adds 0d51797 initial source code. It is BUGGY!
adds 7d22a01 bgzip is more like gzip in its command-line interface
adds dcd2f78 * tabix-0.0.0-1 (r500) * apparently working
adds e0afbb5 * tabix-0.0.0-2 (r501) * accelerate ti_readline()
adds 0f56c58 * tabix-0.0.0-3 (r502) * support meta lines (not tested) * I am going to make the index file in the BGZF format
adds 05df526 * tabix-0.0.0-4 (r503) * index files are bgzf compressed
adds e7dc13d * tabix-0.0.0-5 (r504) * fixed a critical bug in fetching data (a typo in fact) * support SAM (tested on ex1.sam) and VCF (not tested) * improve the command-line interface
adds 446b6e4 documentation
adds f667bfc Release tabix-0.1.0
adds a2d85ec Release tabix-0.1.1
adds 81170d8 * tabix-0.1.3 (r543) * fixed another off-by-one bug
adds f79c886 removed a line of debugging code
adds 15159c7 Added the -l option for listing chromosomes
adds ac9fc9f Fix in src/dst file detection and slight change of behaviour
adds 7cacea8 The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
adds 79d6239 * added the format specification * fixed a typo in bgzip
adds 4fb1b67 * tabix-0.1.3-2 (r555) * do not overwrite index file by default * a little code cleanup
adds 9b14f2c * tabix-0.1.3-3 (r556) * fixed a small memory leak in knetfile * fixed a minor bug for remote downloading
adds 9f16a45 Release tabix-0.1.4 (r559)
adds 50f5b5c * Release tabix-0.1.5 (r560) * Improve seeking efficiency. Index file needs to be rebuilt.
adds cf389c2 If nothing bad happens, this will become 0.1.6
adds c6770bb Release tabix-0.1.6
adds 6fa709d * improved C/Perl APIs * added test for Perl * added an tiny example
adds bccdc09 Release tabix-0.2.0
adds a79e73a Release tabix-0.2.1
adds a39b546 Release tabix-0.2.2
adds 31c8bd3 Complain about not-bgzipped files and check for noncontinuous chromosome blocks
adds 07f01ed Fix: Exit with an error rather than segfault when index is not present and region is queried
adds 3c60871 fixed a bug in C/Java when n_off == 0
adds 128523b patches by Peter Chines
adds 2c0b7ee Added -h option to print header lines
adds 4a6e786 Disable "unknown target name or minus interval" warning.
adds bbcc0b2 Release tabix-0.2.3
adds 08d08a2 Prevent the common user mistake and check the timestamps of the vcf and index file
adds 4dedb83 Fix: Complain only when VCF is newer, not newer or same mtime
adds 1cdcb39 New -r (reheader) option for efficient header replacement.
adds 7d48a19 BED support
adds 70e9ba8 update to the latest bgzf.*
adds 87f69fe fixed two bugs due to recent changes
adds e4477ce update version number
adds 046c761 Release tabix-0.2.4 (r949)
adds bec709b Release tabix-0.2.5 (r964)
adds 8ff4c17 Querying remote files required -f option on some systems
adds 83afb06 updated BGZF
adds 46b2463 Added option for printing header lines only
adds c2a5899 Guess the filetype from the file extension when -p not given
adds 8abdff6 Assume GFF format when the file type cannot be guessed, as in the previous version
adds a33c73e Even better, do this only for reading
adds 1344d39 Fix: allow custom formats
adds f14716c More informative error message about missing or out-of-date tabix index
adds 8af2d0a Fix: do not drop first record with both -B and -h
adds a09bef9 -C to output lines not overlapping BED
adds c49a4ec bgzip now compiles
adds cf03c20 Use htslib's bgzf.h, faidx.h, and razf.h
adds 90ae62f Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
adds 716070d tview and bgzip: Check that the files are bgzipped, not gzipped.
adds 5c1e1bb bgzip: Do not overwrite input files when -b or -s are given
adds 0f9a088 Check return status of IO calls to prevent gcc 4.6.3 warnings
adds ec581d6 Merge tabix and samtools bgzip.c and tabix.c
adds 1d963d7 Initial version of bgzip and tabix with htslib.
adds f38b5e2 Merge bgzip.c and tabix.c/.1 history from github.com/samtools/tabix
adds e45b3f3 Fix bgzip and tabix dependencies and link commands
adds 35f4642 Exit statuses are non-negative
adds 5adb883 bcf_subset: Reset n_fmt fields when all samples are dropped
adds 6e2ebc4 synced_reader: Regions operate on two as well as three columns again
adds db8055a bcf1_sync: Update rlen for new records as well
adds 41e8793 Merge branch 'bcftools+calling' into develop
adds 104adb5 Silence -Wstrict-prototypes warning
adds 996b3c0 Check sam_open() and sam_close() return values
adds 1ce5791 bcf_write: sanity check the number of samples, resolves #55
adds 9ed346d Return "" from bam_flag2str(0) rather than NULL
adds e321182 Bug fix to CRAM indexing and index usage.
adds d3bf5b6 Fixed two small memory leaks.
adds 09ba271 Revert one of the previous memory leaks as it breaks multi-threading. I need to find a more suitable way to solve this. The memory leak is back, but it's tiny; essentially leaking the last (empty) container.
adds eb71ced Better fix for container memory leak.
adds 0557506 Merge CRAM indexing bug fixes (PR #85)
adds 5003f7b Add hts_set_threads() file I/O threading API
adds 70be28c Fix bgzf_write() and bgzf_flush_try() error handling
adds f99d5ba Fix bam_write1() error handling
adds a1fb3bd vcf_parse: Detect missing INFO values in vectors
adds f1f2950 Merge branch 'develop' into bcftools+calling
adds 9db893a For bcftools to work with CSI indexes up to 2^31-1
adds fc4a18b New bcf_hdr_[sg]et_version API; bcf_hdr_subset preserves VCF version
adds 8deb11d Merge branch 'bcftools+calling' into develop
adds dc9a0fe bgzf: Support for reading gzip-compressed files.
adds dd58092 Minor comment change
adds 02721b7 bgzf: Support for FCOMMENT gzip header
adds 165850e bgzf: Support the remaining optional GZIP header fields
adds 2cc7ea4 bcf_sr: New missed_reg_handler and bcf_sr_regions_flush() function
adds d49dfa6 vcf: New bcf_dup() function
adds 191be31 Changed the initial CRAM EOF value to be 1 (expected EOF) and then explicitly set it to 0 at the start of each slice decode.
adds e76b489 idx: Don't create broken .tbi or .csi when file unsorted (VCF/BCF/BAM)
adds 8d283ed Sanitised the setting of fd->empty_container into one place. This also fixes the samtools bug #146.
adds 7d11028 Fix forgotten s/razip/bgzip/
adds b3a7868 Remove RAZF source code
adds e7bd15c Check CIGAR string has fewer than 2^16 operators
adds 7e059de Add a comment to deobfuscate bam_cigar_type
adds b62e668 Fix "unrecognized CIGAR operator" diagnostic
adds be61038 Removed bogus "Unable to find ref name"* errors when converting a SAM file UR:local/path/name syntax and without finding an MD5 reference to use. The code previously went on to work fine as a subsequent refs2id call worked.
adds 6622a18 Add functions for idxstats
adds 885bba0 Improve hts_idx_get_stat to work for more file types
adds 416f02a Return 0/-1 rather than bool; parenthesise C macro
adds d3ec3e2 Merge API functions for index statistics (PR #83)
adds 34082df sam_hdr_write() now calls cram_load_reference if hts_set_fai_filename() has been called. Also refs_load_fai() now copes with being given foo.fa or foo.fa.fai and does the right thing.
adds 0c360be Check index file magic numbers and I/O
adds e8806c7 Fix endianness problems outwith CRAM code
adds 49610fc Set NM/MD creation to be on by default.
adds 97c1e18 synced_reader: Removed unused code
adds aa68a05 vcf: Change of bcf_hdr_add_sample() usage.
adds 252d27d Add sam_open_mode() API function
adds 7d61caf Remove val_unused -- use HTS_UNUSED instead
adds 53c3ba8 bcf_write: Error message instead of assert + propagate the error up
adds 6a5b9fd vcf_parse: Detect incorrect number of columns
adds 6172a08 vcf: Fix BCF syncing when only partially unpacked
adds 3cdd62f vcf: Fixes in bcf_translate
adds 0d4e155 bgzf: Do not end prematurely on non-critical Z_BUF_ERROR zlib error
adds c8c5b31 vcf: Fix bcf_hdr_id2hrec, col_type parameter is needed as well
adds aff3226 bcf_trim_als: Propagate error instead of assert
adds 9074f89 bcf_update_alleles: Reference length with INFO/END
adds a969d0f Fix in index initialization
adds 2504243 Fixed bug in bcf1_sync. The main cause of the bug is as follows: bcf_unpack(bcf_rec, BCF_UN_STR); bcf_update_id(bcf_rec, id); This causes bcf_rec->d.shared_dirty to be set. duplicate = bcf_dup(bcf_rec); This calls bcf1_sync(). Since bcf_rec->d.shared_dirty is set, the shared data is re-created in tmp.s, bcf_rec->shared.s is freed and bcf_rec->shared.s = tmp.s. However, bcf_rec->unpack_ptr and bcf_rec->d.info[i].vptr still point to the old shared.s region which is inv [...]
adds 3b87c0e Improved bug fix of bcf1_sync() from the commit 2504243:
adds 049f877 synced_reader: Consider non-variant sites as matching in comparisons
adds c158790 Add extern "C" around API to enable C++ linking
adds 5f406e5 Merge pull request #108 from MauricioCarneiro/develop
adds eb27d19 vcf: Detect broken structured header lines
adds 7d31af0 synced_reader: Logical complements of target regions
adds 663b9cf bgzf: Translate windows line endings
adds 56d740e bcf_hdr_combine: Check for tags of conflicting lengths
adds 642783e faidx: Exit with an error if run on gzip-ed files
adds cc23df1 Fixed REF_PATH to handle URLs better.
adds 42775eb Suppress compression suffix search on default EBI MD5 service
adds b7c2a46 Merge REF_PATH fixes and libcurl removal (PR #111)
adds fcd0bd8 vcf: Support for mpileup's symbolic <X> allele
adds 894ebcf On open failure, set errno instead of printing message
adds 5498c0a Expose bcf_hdr_parse
adds ac4f30f vcf: Expose bcf_hdr_sync() and hrec_add_idx()
adds e12c343 vcf: bcf_hdr_get_hrec() interface made more general
adds b039db8 mpileup: Support for cigar operator "P"
adds 51d9560 faidx: new faidx_has_seq() call
adds 17d3d47 faidx: Fixed copy-and-paste documentation error
adds 399b580 hts_file_type: correct return of FT_VCF_GZ
adds dedd405 Merge pull request #113 from mcshane/feature/hts_file_type_fix
adds 232b77b Don't call freeaddrinfo() when getaddrinfo() fails
adds 4b024e1 Bug fix in bcf_trim_alleles()
adds c95dbc5 mpileup: Support for cigar operation N
adds dde9bdb Rationalise include guard macro names
adds 949d267 Ensure installation directories are world-executable
adds 19b5a8e Omit control files and README.md from release tarballs
adds 7dcaf17 Add license file
adds 45aaa8b Add MIT/Expat license boilerplate
adds 8b17b24 Fix copy/pasto
adds aaf99a9 Files under cram/ are BSD-licensed
adds deecae2 Add copyright notices and licensing boilerplate
adds 8bb77cc Add klib copyright notices and licensing boilerplate
adds cf35bd6 Add copyright notices and licensing boilerplate
adds b61c691 Add copyright notices and licensing boilerplate
adds 5cb1182 Update copyright notices to reflect historic changes
adds 0b6597c Add copyright notices and licensing boilerplate
adds 9155cca Update copyright years to reflect historic changes
adds d9122b7 Add copyright notices and licensing boilerplate
adds b5fbf05 Add copyright notices and licensing boilerplate
adds 7d3c063 Add copyright notices and licensing boilerplate
adds f19ff09 Add copyright notices and licensing boilerplate
adds 61ad3a6 Add copyright notices and licensing boilerplate
adds 9fc07d5 Merge copyright notice and licensing boilerplate additions
adds e770a1b Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
adds 9e95d31 Link shared library against libm and libpthread
adds 64bebbb Create a pkg-config description for easy linking
adds c99ed6a bgzf_seek: Assign corect block_address (on behalf of Chris Smowton)
adds 0b0736a Add basic INSTALL and README files
adds f2af2ad Release 1.0: first released HTSlib package
adds cc559b8 Merge branch 'master' into debian/unstable
adds 08a1e4a New upstream release; no new license notice.
adds 74b9d7b Build on the master branch.
adds 98c18ca Updated symbols file.
adds 04815a7 New major version (libhts0 -> libhts1).
adds b3a60f2 Remove Debian revision from symbols version.
adds 22fef0c Pass multiarch path to Make. Install pkgconfig file.
adds 8c7f7d4 Replace the old tabix package (from the tabix source package).
adds d3a7098 Dynamically link tabix and bgzip.
adds a9eed75 Prepare changelog.
adds 8aca25f Polish descriptions.
adds 38d7ca9 Statically link tabix and bgzip for the moment.
adds 0141e47 htslib (1.0-1) experimental; urgency=low
adds 8210cf3 htslib (1.0-2) unstable; urgency=medium
adds 1f1e3f6 Merge version number and soname bump from master
adds 1903fd4 Set explicit REF_PATH to make tests self-contained
adds b6934ff Force nul termination of the kstr holding the CRAM index so that sscanf doesn't attempt to check beyond the bounds of the string memory.
adds 3fe4cf8 Ensure hand-made kstring is NUL-terminated
adds 89e267a Ensure items to be installed are built and up-to-date
adds 546bfcb vcf: Output "." not "nan" in scalar INFO fields
adds 6af42b1 vcf: separate header lookup from field getter
adds 410cf54 Merge pull request #127 from broadinstitute/broad_header_lookup
adds 6c6c75b Make hts_idx_push no longer return 0 after the first unmapped read. This fixes idxstats
adds ebbad4b Merge pull request #124 from dpryan79/develop
adds 830ea73 faidx API to access sequence stats
adds 20558bc bcf_get_info_values: Return correct INT8 and INT16 missing value
adds cf4eab0 Minor documentation update
adds 575be14 Correct reference lines
adds 3f30883 Removed the .gz, .Z, .sz etc suffix searching when looking for reference files.
adds d25c678 Remove the | from the default REF_PATH.
adds fa6011a bgzf: Write plain gzip files if is_gzip set
adds dcefe5b Don't install libhts.so.1 as a man page
adds 5a0ee03 Release 1.1: various minor bug fixes
adds 1357fbd Merge tag '1.1' into debian/unstable
adds be365db New upstream release, no new copyright nor license notice.
adds 87549cd Updated symbols file.
adds 873ea9b Removed orphan paragraph.
adds 49de2b9 Allow parallel build.
adds 7fe3bb5 Normalise source package control file (VCS-Browser, Pre-Depends).
adds 0e5e9e6 Conforms to Policy 3.9.6.
adds 15eac2b htslib (1.1-1) unstable; urgency=medium
This update added new revisions after undoing existing revisions.
That is to say, some revisions that were in the old version of the
annotated tag are not in the new version. This situation occurs
when a user --force pushes a change and generates a repository
containing something like this:
* -- * -- B -- O -- O -- O (f65dde0)
\
N -- N -- N refs/tags/debian/1.1-1 (4d788b9)
You should already have received notification emails for all of the O
revisions, and so the following emails describe only the N revisions
from the common base, B.
Any revisions marked "omits" are not gone; other references still
refer to them. Any revisions marked "discards" are gone forever.
No new revisions were added by this update.
Summary of changes:
.gitattributes | 4 +
.gitignore | 22 +
.travis.yml | 8 +
INSTALL | 25 +
LICENSE | 69 +
Makefile | 337 +
README | 5 +
README.md | 17 +
bgzf.c | 1118 +++
bgzip.c | 284 +
changes | 69 -
config.h | 3 +
cram/cram.h | 66 +
cram/cram_codecs.c | 1764 ++++
cram/cram_codecs.h | 155 +
cram/cram_decode.c | 2138 +++++
cram/cram_decode.h | 112 +
cram/cram_encode.c | 2630 ++++++
cram/cram_encode.h | 105 +
cram/cram_index.c | 505 ++
cram/cram_index.h | 98 +
cram/cram_io.c | 3652 ++++++++
cram/cram_io.h | 532 ++
cram/cram_samtools.c | 144 +
cram/cram_samtools.h | 97 +
cram/cram_stats.c | 357 +
cram/cram_stats.h | 59 +
cram/cram_structs.h | 752 ++
cram/files.c | 76 +
cram/mFILE.c | 634 ++
cram/mFILE.h | 88 +
cram/md5.c | 295 +
cram/md5.h | 54 +
cram/misc.h | 110 +
cram/open_trace_file.c | 351 +
cram/open_trace_file.h | 115 +
cram/os.h | 306 +
cram/pooled_alloc.c | 170 +
cram/pooled_alloc.h | 56 +
cram/sam_header.c | 1222 +++
cram/sam_header.h | 452 +
cram/string_alloc.c | 153 +
cram/string_alloc.h | 69 +
cram/thread_pool.c | 713 ++
cram/thread_pool.h | 197 +
cram/vlen.c | 432 +
cram/vlen.h | 48 +
cram/zfio.c | 185 +
cram/zfio.h | 54 +
debian/changelog | 38 +
debian/compat | 1 +
debian/control | 61 +
debian/copyright | 117 +
debian/gbp.conf | 15 +
debian/htslib-test.install | 1 +
debian/libhts-dev.install | 6 +
debian/libhts1.install | 2 +
debian/libhts1.symbols | 534 ++
debian/rules | 28 +
debian/source/format | 1 +
debian/source/options | 1 +
debian/tabix.install | 2 +
debian/tabix.links | 1 +
debian/tabix.manpages | 1 +
debian/watch | 3 +
dsc | 47 -
faidx.5 | 147 +
faidx.c | 473 +
hfile.c | 526 ++
hfile_internal.h | 75 +
hfile_net.c | 99 +
hts.c | 1356 +++
htslib.mk | 144 +
htslib.pc.in | 10 +
htslib/bgzf.h | 314 +
htslib/faidx.h | 135 +
htslib/hfile.h | 204 +
htslib/hts.h | 330 +
htslib/hts_defs.h | 47 +
htslib/kfunc.h | 75 +
htslib/khash.h | 617 ++
htslib/khash_str2int.h | 124 +
htslib/klist.h | 121 +
htslib/knetfile.h | 101 +
htslib/kseq.h | 253 +
htslib/ksort.h | 285 +
htslib/kstring.h | 270 +
htslib/sam.h | 426 +
htslib/synced_bcf_reader.h | 290 +
htslib/tbx.h | 77 +
htslib/vcf.h | 880 ++
htslib/vcf_sweep.h | 39 +
htslib/vcfutils.h | 112 +
htslib_vars.mk | 38 +
kfunc.c | 280 +
knetfile.c | 633 ++
kstring.c | 254 +
sam.5 | 68 +
sam.c | 1822 ++++
synced_bcf_reader.c | 1215 +++
tabix.1 | 155 +
tabix.c | 399 +
tbx.c | 315 +
test/aux#aux.sam | 5 +
test/aux.fa | 2 +
test/aux.fa.fai | 1 +
test/c1#bounds.sam | 4 +
test/c1#clip.sam | 8 +
test/c1#pad1.sam | 10 +
test/c1#pad2.sam | 14 +
test/c1#pad3.sam | 14 +
test/c1.fa | 2 +
test/c1.fa.fai | 1 +
test/ce#1.sam | 2 +
test/ce#2.sam | 3 +
test/ce#5.sam | 11 +
test/ce#5b.sam | 12 +
test/ce#large_seq.sam | 3 +
test/ce#tag_depadded.sam | 11 +
test/ce#tag_padded.sam | 11 +
test/ce#unmap.sam | 6 +
test/ce#unmap1.sam | 20 +
test/ce#unmap2.sam | 29 +
test/ce.fa | 20803 +++++++++++++++++++++++++++++++++++++++++++
test/ce.fa.fai | 7 +
test/compare_sam.pl | 172 +
test/fieldarith.c | 72 +
test/fieldarith.sam | 15 +
test/hfile.c | 204 +
test/sam.c | 143 +
test/test-vcf-api.c | 235 +
test/test-vcf-api.out | 28 +
test/test-vcf-sweep.c | 112 +
test/test-vcf-sweep.out | 4 +
test/test.pl | 202 +
test/test_view.c | 151 +
test/test_view.pl | 71 +
test/xx#blank.sam | 0
test/xx#large_aux.sam | 4 +
test/xx#large_aux2.sam | 11 +
test/xx#minimal.sam | 10 +
test/xx#pair.sam | 7 +
test/xx#rg.sam | 13 +
test/xx#triplet.sam | 7 +
test/xx#unsorted.sam | 8 +
test/xx.fa | 5 +
test/xx.fa.fai | 2 +
upload | 9 -
vcf.5 | 120 +
vcf.c | 3167 +++++++
vcf_sweep.c | 182 +
vcfutils.c | 666 ++
152 files changed, 60949 insertions(+), 125 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .gitignore
create mode 100644 .travis.yml
create mode 100644 INSTALL
create mode 100644 LICENSE
create mode 100644 Makefile
create mode 100644 README
create mode 100644 README.md
create mode 100644 bgzf.c
create mode 100644 bgzip.c
delete mode 100644 changes
create mode 100644 config.h
create mode 100644 cram/cram.h
create mode 100644 cram/cram_codecs.c
create mode 100644 cram/cram_codecs.h
create mode 100644 cram/cram_decode.c
create mode 100644 cram/cram_decode.h
create mode 100644 cram/cram_encode.c
create mode 100644 cram/cram_encode.h
create mode 100644 cram/cram_index.c
create mode 100644 cram/cram_index.h
create mode 100644 cram/cram_io.c
create mode 100644 cram/cram_io.h
create mode 100644 cram/cram_samtools.c
create mode 100644 cram/cram_samtools.h
create mode 100644 cram/cram_stats.c
create mode 100644 cram/cram_stats.h
create mode 100644 cram/cram_structs.h
create mode 100644 cram/files.c
create mode 100644 cram/mFILE.c
create mode 100644 cram/mFILE.h
create mode 100644 cram/md5.c
create mode 100644 cram/md5.h
create mode 100644 cram/misc.h
create mode 100644 cram/open_trace_file.c
create mode 100644 cram/open_trace_file.h
create mode 100644 cram/os.h
create mode 100644 cram/pooled_alloc.c
create mode 100644 cram/pooled_alloc.h
create mode 100644 cram/sam_header.c
create mode 100644 cram/sam_header.h
create mode 100644 cram/string_alloc.c
create mode 100644 cram/string_alloc.h
create mode 100644 cram/thread_pool.c
create mode 100644 cram/thread_pool.h
create mode 100644 cram/vlen.c
create mode 100644 cram/vlen.h
create mode 100644 cram/zfio.c
create mode 100644 cram/zfio.h
create mode 100644 debian/changelog
create mode 100644 debian/compat
create mode 100644 debian/control
create mode 100644 debian/copyright
create mode 100644 debian/gbp.conf
create mode 100644 debian/htslib-test.install
create mode 100755 debian/libhts-dev.install
create mode 100755 debian/libhts1.install
create mode 100644 debian/libhts1.symbols
create mode 100755 debian/rules
create mode 100644 debian/source/format
create mode 100644 debian/source/options
create mode 100644 debian/tabix.install
create mode 100644 debian/tabix.links
create mode 100644 debian/tabix.manpages
create mode 100644 debian/watch
delete mode 100644 dsc
create mode 100644 faidx.5
create mode 100644 faidx.c
create mode 100644 hfile.c
create mode 100644 hfile_internal.h
create mode 100644 hfile_net.c
create mode 100644 hts.c
create mode 100644 htslib.mk
create mode 100644 htslib.pc.in
create mode 100644 htslib/bgzf.h
create mode 100644 htslib/faidx.h
create mode 100644 htslib/hfile.h
create mode 100644 htslib/hts.h
create mode 100644 htslib/hts_defs.h
create mode 100644 htslib/kfunc.h
create mode 100644 htslib/khash.h
create mode 100644 htslib/khash_str2int.h
create mode 100644 htslib/klist.h
create mode 100644 htslib/knetfile.h
create mode 100644 htslib/kseq.h
create mode 100644 htslib/ksort.h
create mode 100644 htslib/kstring.h
create mode 100644 htslib/sam.h
create mode 100644 htslib/synced_bcf_reader.h
create mode 100644 htslib/tbx.h
create mode 100644 htslib/vcf.h
create mode 100644 htslib/vcf_sweep.h
create mode 100644 htslib/vcfutils.h
create mode 100644 htslib_vars.mk
create mode 100644 kfunc.c
create mode 100644 knetfile.c
create mode 100644 kstring.c
create mode 100644 sam.5
create mode 100644 sam.c
create mode 100644 synced_bcf_reader.c
create mode 100644 tabix.1
create mode 100644 tabix.c
create mode 100644 tbx.c
create mode 100644 test/aux#aux.sam
create mode 100644 test/aux.fa
create mode 100644 test/aux.fa.fai
create mode 100644 test/c1#bounds.sam
create mode 100644 test/c1#clip.sam
create mode 100644 test/c1#pad1.sam
create mode 100644 test/c1#pad2.sam
create mode 100644 test/c1#pad3.sam
create mode 100644 test/c1.fa
create mode 100644 test/c1.fa.fai
create mode 100644 test/ce#1.sam
create mode 100644 test/ce#2.sam
create mode 100644 test/ce#5.sam
create mode 100644 test/ce#5b.sam
create mode 100644 test/ce#large_seq.sam
create mode 100644 test/ce#tag_depadded.sam
create mode 100644 test/ce#tag_padded.sam
create mode 100644 test/ce#unmap.sam
create mode 100644 test/ce#unmap1.sam
create mode 100644 test/ce#unmap2.sam
create mode 100644 test/ce.fa
create mode 100644 test/ce.fa.fai
create mode 100755 test/compare_sam.pl
create mode 100644 test/fieldarith.c
create mode 100644 test/fieldarith.sam
create mode 100644 test/hfile.c
create mode 100644 test/sam.c
create mode 100644 test/test-vcf-api.c
create mode 100644 test/test-vcf-api.out
create mode 100644 test/test-vcf-sweep.c
create mode 100644 test/test-vcf-sweep.out
create mode 100755 test/test.pl
create mode 100644 test/test_view.c
create mode 100755 test/test_view.pl
create mode 100644 test/xx#blank.sam
create mode 100644 test/xx#large_aux.sam
create mode 100644 test/xx#large_aux2.sam
create mode 100644 test/xx#minimal.sam
create mode 100644 test/xx#pair.sam
create mode 100644 test/xx#rg.sam
create mode 100644 test/xx#triplet.sam
create mode 100644 test/xx#unsorted.sam
create mode 100644 test/xx.fa
create mode 100644 test/xx.fa.fai
delete mode 100644 upload
create mode 100644 vcf.5
create mode 100644 vcf.c
create mode 100644 vcf_sweep.c
create mode 100644 vcfutils.c
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git
More information about the debian-med-commit
mailing list