[med-svn] [htslib] branch master created (now 9469458)
Charles Plessy
plessy at moszumanska.debian.org
Thu Nov 21 08:17:44 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository htslib.
at 9469458 Removed debug command accidentally introduced.
This branch includes the following new commits:
new 3860d63 initial checkin
new 47191a7 finish parsing ## lines
new 2e0e641 header parsing finished (not well tested)
new aac04c8 towards parsing VCF
new 546e607 BCFv2 quick reference
new fe0041e code backup
new b17f2c5 a bit code restructuring
new 7e33530 encode up to the INFO field
new 185b5f5 VCF=>BCF, up to QUAL
new 973a1be bcf->vcf, up to FILTER
new aa7b673 bcf->vcf, up to INFO
new 6caad03 change long to int32_t
new 722124a towards parsing genotype fields (unfinished)
new dde5251 a little code cleanup
new 5cdfa18 parse genotype fields; not tested yet
new 44b011d restructure the code a bit
new e667943 to restructure decoding
new 3274571 restructure decoding
new d6028ed working on printing genotypes; not working yet
new ee9bc0d fixed one bug, more to fix
new 07b4746 working on a toy example!!!
new b3e623b another bug fix
new c2da32c add a very simple CLI for testing
new 1003534 if PASS is not in the hdr, add it
new 6959b7c use two memory buffers to fix a bug
new d663b02 clean bill by valgrind on a toy example
new 4608878 move the memory buffer to the header
new 29015d5 bugfix: extra byte for string
new c70504d read seq dict from an external file
new 9dc290c finished text-in-text-out
new 4c0f791 code backup
new fd1f4f4 bcf->vcf without inferred information
new 7d7ccc4 do not compute inferred info during vcf->bcf
new 1badf87 separate shared and individual annotations
new df8eff4 rename variables
new 2fffb33 added simple cmd interface
new 45be8f4 separated the main function; added Makefile
new baaa3fb add external seq-dict to the header
new a9a6ae4 added git ignore
new 341a947 updated the quick reference
new 976e97f bugfix: -l not working; corner case of Number=.
new 7dbaa13 bugfix: segfault given Number=.
new 75db452 when -l is in use, use binary output
new 791efdf parse Flag type
new f776393 bugfix: in case of no FORMAT
new a6d5876 added CNL to the example
new 7b74c08 clarified quick reference
new 801bb84 more consistent Flag; code clean up
new 9fedbbc do not keep '\0' in sample strings
new 81ee0f0 cleanup
new 8901681 allow arrays longer than 128
new 8bf3593 bugfix: missing "," in ALT
new c62466e use three header hash tables instead of one
new 5ab4fd8 rename variables
new ceeff19 added line counting
new caccb02 routine to unpack FORMAT
new 4081e7f collect site allele count
new 0860358 fixed a memory leak
new d1ac9b6 supposedly faster VCF parsing
new ac25a3f minor
new 3f59614 can be compiled with g++
new 6a3a99a bugfix: str in GT not encoded properly
new 3127025 bugfix: incorrect float
new 85d1be2 move alloca() upwards
new b418823 code backup; not working!
new ba388a1 parse n_sample from record lines
new 634d84d back to work
new b37f9f8 encode GT
new bb530e2 phasing info stick to the allele behind
new b53a61c updated BCFv2 spec
new cd33690 merge REF and ALT
new d0cab9e added GT encoding
new 92290e0 updated to the latest BGZF
new df356d2 bugfix: prematured output in bgzf-mt
new 3c2af63 g++ errors in bgzf-mt
new 9dc247b prepare to add sam parsers
new 9b66553 separate file I/O
new 55d181a use hts.{h,c} in vcf
new 0c7db5d replace vcf_verbose with hts_verbose
new c644e21 BAM I/O, SAM output; not tested
new 72432b3 compiling err/warning from g++
new 530ba16 create separate directory
new f233c19 rename api to htslib
new feb86e1 added sam interface; not working
new df979ba bugfix: wrong returned value from knet_seek()
new b463806 code backup; NOT compiling
new 6d004ce compiled, but certainly not working
new a4f0bdf working, up to QUAL
new b8f1d57 SAM parser works on a toy example
new 56d7ddb report line number
new 6375f0c use hts_getline() to keep line number
new b42cc73 bugfix: wrongly parse B arrays
new 32561b4 added a SAM example
new d8ddcc0 do not check CIGAR if CIGAR==*
new e546ed8 bugfix: uninitialized numbers
new 75e3bd9 bugfix: compute "bin" in bam
new 9532488 code backup
new b954f55 added comments
new b09fcae code backup
new f9cb9cc code backup
new 93df7a9 minor changes
new e3e6d3b code backup
new eab97ae separate indexing from hts.c
new d27cec6 bam index interface
new a631896 index load; bugfix: wrong offset of last chr
new 4dd932e code backup
new bb83110 add region parser (not tested)
new b8733af code backup
new 20ba14c indexing apparently works for BAM
new 144b7ef bugfix: one extra record from random access
new 7ec64b1 fix C++ compiling errors and warnings
new 18ac806 code cleanup
new b733d9c removed sam_hdr_t::has_SQ
new 6053079 added the pileup/mpileup interface
new 2244809 fixed g++ warnings
new b6f6440 automatically figure out the index file name
new 20c7222 forgot to add Makefile
new 99f4547 expose bgzf.h
new 6e20b48 bamshuf: shuffle BAM
new f06e1e3 added bam2fq
new c9bda2f System may have an <endian.h>; merge to hts.h
new 8efb052 fixed gcc warnings
new 962a3a5 added simplified stdint.h, in case it is missing
new b16b96b bam2fq: output SE reads in the PE mode
new 16275c3 output the number of reads
new 0313740 bugfix: bamshuf not working when collision
new 09ee5a0 make BCF APIs similar to BAM APIs
new b92ee1d added Description to PASS
new 9bf881e detailed vcfview cmd prompt
new 32f4466 bam2fq: change the option name
new c69050d generalize the BAM index
new 79e477b unified index seems to work; optimization needed
new 1426dd5 merge a small bin to its parent
new 13c21f2 fixed a couple of warnings
new ba50fb3 changed magic
new 9aabfc0 bugfix: parent merging not working
new fb88ba9 reduced the min chunk size
new bfcfcda BCF2 index; compiled but not working
new e8ad97c BCF index working on a toy example
new 2d1090c allow longer arrays
new df19476 allow missing binary index
new 20e7996 wrong n_lvls
new e4813e9 bugfix missing string not printed properly
new 0044a03 avoid printing "\0" in the header
new 1b6136c replace 0x7F800001 with bcf_missing_float
new 07790f2 stop if not sorted
new 51542f0 code backup; NOT working
new bc5a869 a bit code cleanup
new 1291adc code cleanup
new b9b4afa bugfix: hts index not working when n_seq is unknow
new 09db228 CLI for tabix
new 9b5fcbd tabix apparently works, at least on toy examples
new 6ed05de added an example for tabix
new 73afb81 format of the new index
new dc46744 minor change to the index description
new eda81c1 fixed a few g++ warnings
new 67f0b9d added command-line help
new f355744 added a brief README
new cc7b3c0 more flexible about the '\n' and '\0' in hdr
new f73f662 bugfix: wrong integer packing
new 97dbfb0 change the meaning of l_shared (in line with GATK)
new d5b55bc output a subset of samples
new 3cb1f4b allow to drop all individual information
new ffc8d65 smart sample list
new 9ea927a bugfix: missing values are not filled sometimes
new 38296d0 new indexing algo/fmt; NOT working yet
new 0fd291d BAM indexing works again on a toy example
new 08c8bb5 bugfix: bin 0 is not sorted
new 112176a a bit code cleanup
new 73bc25e bugfix in the new index; containing dbg code
new be1e4c1 bugfix
new c6e9c5f using -O2
new cf0da03 bugfix: update_loff() run twice
new a9388b0 handle unmapped aln in SAM
new 03ec23b halve HTS_MIN_MARKER_DIST; updated doc
new 2954e1d declare bcf_fmt_sized_array() in the header
new b1512c1 unpack bcf1_t; NOT WORKING yet
new f71e2c1 nothing
new d185fc6 declare bcf_unpack in the header
new b35d09a Merge pull request #2 from arq5x/master
new 200b841 generating vcf from bcf_dec_t; to remove old code
new c1c36bf removed old vcf_format1() code
new 3110062 bugfix: a typo
new cac07ac a little bit code simplification
new 8fe0f48 make bcf_unpack() more flexible
new 8d62aaf changed function names
new 5683533 added a little doc
new 1f23f2b migrate sam2break.d to htslib
new 87ab8c0 abreak is working!
new 2633148 better help
new 6c7bfff vcf<->bcf is pretty mature now
new 92a96c9 compatible with tabix index
new 49b0749 bugfix: vcfview -G failing due to recent changes
new 6d05f18 API to test if a record is a SNP
new bb3e0b9 Experimental implementation of vcfcheck (non-functional)
new f58b777 Fill sequence dictionary from tabix index if contigs not present in VCF header. Synced reader basically working. (No alleles detection yet.)
new a564bfe Functional implementation of synced reader including allele checking
new 33b6f03 Collect Ts/Tv by AF
new d133a54 Synced reader can collapse sites by variant type; new API call set_variant_types
new c8f1555 Invalid read fix in hts_itr_query; Unsafe loop limits fix in vcf_parse1
new 8999bf8 Removed hacky work around, tabix seems to be fully working now
new 897f9d1 First plot-vcfcheck skeleton
new 5508b9c Merge branch 'master' of github.com:pd3/htslib
new 8de0693 Calculate AC,AN on fly if not in INFO; allow calling bcf_unpack() repeatedly without redoing the work; plot graphs using matplotlib; bugfixes
new 621aeb7 Calculate AC,AN on fly if not in INFO; allow calling bcf_unpack() repeatedly without redoing the work; plot graphs using matplotlib; bugfixes
new 5e236ad Use matplotlib and pdflatex to create summary slides
new 17acc9e More stats: indel distribution and substitution types
new b364964 More stats: SNP and indel counts by AC
new 9b6b318 added BAM aux functions and bam2bed
new 1fa4c89 bugfix: invalid memory access (fixed by petr)
new dce457b create_pdf: Switched from slides class to memoir
new 5b98268 vcf: add "PASS" before anything else
new faeb779 clarify the BCF2 document
new cffe2b6 clarify that BCF2 is BGZF'd and little endian
new 5fb5791 More stats: frameshifts ratio; bug fixes
new 5dfae19 Merged github.com:pd3/htslib
new 2d16106 Documented the synced reader; More stats for vcfcheck: genotype concordance; Bugfixes
new c201d5a More vcfcheck stats: Ts/Tv and nHets by sample
new 09f4cb6 Another vcfcheck stats: NRD by sample
new c251364 Fix in per sample stats; Minor cosmetic improvements of plots
new dff6a2b Sample list from file or command line; Handle missing GTs in calc_ac and init_iaf; Documented plotting
new 07ae6f2 Changed NRD output
new 2f3e234 New option --split-by-ID for known vs novel stats
new 0a200b4 r198: changed the BCF2 magic to BCF\2\1
new 23a1aa4 Fix in calc_ac for missing GTs; Number of MNPs and other events in the summary table
new 3a3c878 Always check INFO/AC,AN for by AF; TsTv by Qual stats
new c8bdd76 r199: support retrieving reads w/o coordinates
new 633f436 Depth distribution stats
new 46a866f Fix function prototypes for knetfile and bgzf to match system read and write.
new b8014e6 Use off_t and lseek rather than the 64 alternatives as this is more portable.
new 22543d6 Fixed typo, open with w instead of r
new c2a68d3 Fixed typo, check i-th ALT instead of 1st in set_variant_types
new 283cefe Synced reader and hence vcf*tools now work also with bcf2
new c63f2ec Merge remote branch 'main/master'
new 7be5993 Merge remote branch 'mp15/misc_improve'
new 959db8d Merge pull request #1 from samtools/master
new 76bc90d Fix signed return going into unsigned variable
new fc41e37 Make nucleotide tables const
new 31e76af Amend .gitignore to ignore produced binaries
new 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
new f56ce9a Bug fix: variant type not checked in the absence of --collapse option, this affected all vcf* commands
new 2253b7e Changed order of underscore escaping and line breaking to prevent loss of escape characters
new e9a0809 In calc_ac check added for different BCF_BT_INT* types; New trim_alleles method
new 97e758e Fix in variant type recognition: distinguish indels from complex events
new e79542f Plotting Hets vs Homs instead of plain Hets; Sanity check for FS section header
new 39d404b Add missing contigs to the header permanently
new 55157de Removed repeated call of bcf_unpack_fmt_core in vcf_format1
new 922e9c1 New API routine: remove_alleles; get_fmt_ptr
new 626d874 New API routine: remove_alleles; get_fmt_ptr
new 6b262e1 New API routine: remove_alleles; get_fmt_ptr
new 1302894 Do not attempt to read directories in bcf_sr_set_samples
new 6f59a40 Use uint64_t for DP stats. On behalf of Chris: plot-vcfcheck can now merge per-chromosome vcfcheck files.
new 8c3471e Fixed a typo which rendered -n <cnt> ineffective.
new 6c66de8 New -C, --complement option for vcfisec. bcf_seqnames now returns chromosomes in correct order
new e29e94c Temporary changes
new f0e6fec tmp save
new 5a57ff4 GT merging now functional
new 1b554a4 r200: keep read index in bam1_t
new aaaa18b Sanity check allow output from both vcfcheck and plot-vcfcheck -m
new 5c19e1f Allow missing values in lists in VCF output
new 3563310 Most features of vcfmerge functional now.
new 1bc5f6f Merge branch 'master' of github.com:pd3/htslib
new 2d9a6cb merge_format_field: fix in setting missing values
new 3b64be1 Fixed memset error in vcfmerge
new 8055bae Fix in merge_alleles (expand REF if necessary); Normalize local copy of ALT,REF
new ab2a27c plot-vcfcheck: New --rasterize option for fast PDF rendering
new 755907e plot-vcfcheck: fixex merging of per-sample stats
new 095c00c vcf_parse1: error recovery on missing FILTER/INFO/FORMAT tag definitions
new e25fb12 vcfcheck: New stats and graph, allelic r2 by AF
new ebc767a plot-vcfcheck: fixed forgotten .pdf extension string
new 7dfbbe8 Merge remote branch 'remotes/mp15master/master' into develop
new d000f83 plot-vcfcheck: removed forgotten debugging comments; merge of allelic r2 column in GCsAF
new 6a903ed plot-vcfcheck: -T option to set PDF title; minor improvements in various plots
new e207c50 htscmd: fall back to default name when named non-standardly
new 5258aaa vcfcheck: singletons by sample and multiallelic SNPs stats
new 60c60d8 plot-vcfcheck: new -s switch; several new graphs and table values
new 92217e5 vcf.c: strip newline from the last sample in BCFs
new 4d7c161 plot-vcfcheck: Added missing legend into SNP/indel counts by AF graphs
new 3d24cd5 plot-vcfcheck: Fix in merging per-sample average depth - average, not sum
new 1208a13 Merge remote branch 'remotes/pd3master/master' into develop
new 3894559 htslib/vcf.c: Set length of on-fly added chromosomes to max signed int; Removed deprecated header parsing code.
new b238605 plot-vcfcheck: zoomed y-range for ts/tv by sample graph
new 420881b htslib/vcf.c: free unused records, fixed a small memory leak
new 6185a7b vcfcheck: New -t option
new 145e599 vcfcheck: --debug outputs to stdout rather than stderr and the output parsable
new 2340eda Merge branch 'master' of github.com:samtools/htslib
new baaee35 merge r199 changes; part 1
new cb0c9af merge r199 changes; part 2
new c0c76dd merge r199 changes; part 3
new 317adce added bam2bed
new 7ec0534 r198: tag version
new ea42b99 r199: reduce one conflict when merged with master
new 69cf929 r200: the previous is not good enough
new 85850c1 plot-vcfcheck: Prevent division by zero in FS merging
new 88ee406 plot-vcfcheck: Escape all underscores summary.tex
new 7581e65 Exported some routines
new b57e308 Allow to skip errors
new eaa78d2 Append new header lines
new ba60d62 Merge remote-tracking branch 'upstream/master'
new db4acc0 Add .gitignore for LaTeX to doc directory
new 781eb46 Merge remote branch 'remotes/mp15master/master' into develop
new 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!
new 1177f60 Merge branch 'develop' of github.com:samtools/htslib into develop
new e179827 New tool: vcfquery. (TODO: sample columns)
new 0eb64b0 calc_ac in vcfutils: return when AC present in header but absent in the line
new d38cede New tools: vcfquery, vcffilter (SOM)
new e918535 vcffilter: Allow fixed threshold filtering of annotations which are not used in SOM
new 51ddaa0 vcffilter: added check if supplied annotations are unique
new a63f58a vcfquery: print header only when requested
new 1f12f86 Fix handling of legacy tabix indexes with empty dictionary.
new c067874 Merge pull request #7 from mp15/master
new 2afe338 vcfcheck hotfix: Handle properly sample stats, cases where AC,AN are present in the header but not in the lines
new 882af47 Merge branch 'develop' of github.com:samtools/htslib into develop
new e248154 gtcheck: New tool, initial commit
new d6e7be5 htslib/vcf.[hc]: Keep ID separately from the alleles block. Renamed synced_bcf_reader data structures and functions.
new aa32b80 Added faidx into htslib
new fac764a Merge branch 'develop' of git://github.com/samtools/htslib into develop
new 24fd203 vcfquery: Read multiple VCFs from a file.
new bda1c25 Merge branch 'develop' of github.com:samtools/htslib into develop
new 30219e0 vcffilter: allow filtering of split VCFs with -r
new ad34679 vcfquery: forgotten open call with -l
new d98a119 do not round per-sample average depths to integer values
new a2d192f gtcheck: better output file names with -p dir/ prefix.
new 1f32fe6 gtcheck: Print header in the "-s and no -p" mode.
new 31c3a44 norm indels: backup commit
new 0a596c5 Merge remote branch 'remotes/origin/develop' into norm-indels
new 4987a94 vcfnorm: New command for normalizing and left-aligning indels.
new 5f16541 Merge branch 'develop' of github.com:samtools/htslib into develop
new 17765c6 vcfquery fix: throw an error when no VCF given with -l.
new 60f4eac vcfgtcheck fix: added the command into main()
new a8e4773 Merge pull request #8 from sm15/develop
new 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.
new cc0285e Merge branch 'master' of github.com:samtools/htslib
new 5963c16 Updated test file for vcfcheck
new d191f5e vcfnorm fix: segfault on nasty case of indel; synced_reader fix: read from stdin
new 5d91d67 vcfnorm: Sanity check for reference sequence mismatches
new b6ebfdb added this missing file
new 078817b Merge branch 'lite'
new cd6a15d bam2fq: skip secondary alignments
new 168452f Merge branch 'lite'
new 3fcccf2 Bugfix: core is a member of bam1_t->core
new 5e9cebd Merge pull request #9 from kmsquire/fix_secondary_check
new b89ba2f compiling error
new 7e47a55 vcfnorm: Bugfixes, more robust realignment, more sanity checks.
new d9ae9b4 Merge branch 'master' of github.com:samtools/htslib
new 0831df4 vcf_format1: move the string initialization outside so that the method can work in append mode (used by vcfquery)
new 3c309c8 synced_reader: Allow reading of unindexed .vcf and .vcf.gz in more situations
new 1f9cd24 vcfquery: Do not crash when no arguments given
new 0d29f5d vcf.[hc]: convenience routine for converting BCF_INT types into C ints
new d64ba91 vcfgtcheck: new functionality - multi-sample cross-check of genotypes
new 996f0de bcf_set_iarray: fix in incrementing typed pointer
new 7f5b3e6 gtcheck: added per-sample depth plot
new aecef4d vcfgtcheck: Slight change in semantics, -g now used only for the known genotypes.
new 5cba9d8 bcf core lib: PASS filter must come first in order to conform to BCF specification
new 851df67 bcf core lib: Fixed a silly bug from the last commit. FILTER=PASS indeed must come first, but only after the ##fileformat string.
new 6d906ba core vcf: added API for modifying/deleting/adding INFO fields, currently only VCF output supported; vcfmerge: AN,AC tags now updated correctly.
new 5b0880e vcfcheck: Do not crash at non-variant sites. Restore checking of two VCFs.
new 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 [...]
new eef8320 gtcheck: Removed forgotten debugging line
new 73f147b A few bugfixes from the previous two commits. New -S option in gtcheck and -H made work also in the cross-check mode
new 2f5843a vcfquery fix: Allow a mask file with the -v option
new d09058b vcfcheck: complain if tabix index not available with -t option
new 7141bd5 vcfcheck: Do not run in streaming mode with the -t option
new 4cf9350 vcffilter: fixed a typo, output file names now named correcly based on filter type
new 84901c3 bcf1_update_info fix: initialize bcf_info_t pointer, do not pass NULL
new d01fcee vcffilter: extended help message
new 19ca371 vcffilter: allow arbitrary order in -f and -l filtering options (X>value is same as value<X)
new b1c5fea vcffilter: plot annotation distributions
new eaee02d vcfview: Restored the subset functionality
new aae973b vcfview: Restored the subset functionality (continued)
new 1ed4f54 vcfmerge: do not crash with non-overlapping chromosomes
new 54868e8 vcffilter: Plot also cropped annotation distributions to show the range of values actually used in filtering
new 35ed1b5 vcfgtcheck: Fix in INFO/DP parsing, wrong ID was used before
new 944c4b0 vcfmerge: fix of copy-and-paste error in format field merging, use correct integer ranges
new 89f7e5d gtcheck: fixed incorrect output, instead of uncertainty, the opposite (confidence) was reported before
new 7d76f62 vcffilter: check to prevent division by zero in the python plot script
new 1dbfae8 vcfisec: in the sites output mode print also file mask
new f4bfe4a vcfquery: Enable -p option again
new 6a5a672 vcffilter: Plot also bad sites in annotation distributions. Updated test files.
new 974d20b Fix crash on legacy files
new 46a4b6a Use sizeof() and NULL instead of numbers
new ce6022e Import header comments from samtools
new 99b8b89 Add const to char *'s to ensure they can be called with fixed values without triggering compiler warnings
new 5d717a2 vcfmerge, vcfisec: Change in synced reader's API, allow unlimited number of input files. (Previously the limit was sizeof(int)*8)
new f6c95a1 Merge remote branch 'mp15/develop' into develop
new ebcc4be optionally output OQ instead of QUAL
new 1c631e9 Merge branch 'lite'
new 429216a vcffilter: backup commit, bad SOM now working
new 12b827f vcfcheck: Fixed a bug introduced by recent changed in synced reader
new 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.
new fb0d88d vcfmerge: Fixed subtle bugs revealed when merging FMT fields of different lengths; Append version string and command to the output VCF header
new 222fe6c vcffilter: First step towards indel filtering - new switch to select from good sites mask
new f344f7a vcffilter: skip the two additional score fields when applying SOM filters
new 8e14b56 vcfcheck: create additional ts/tv stats which counts 1st alternate allele only
new 8b095aa Port fixes from samtools razf.c/h to htslib.
new f15f7bc vcfcheck: More readable output, replace "-" by "<STDIN>" when reading from standard input
new c3622b8 Revert to kstring.h with a separate kstring.c
new a458ed8 Fix <stdarg.h> include
new ac479c3 Merge changes from samtools's kstring
new b281180 vcfview: Fix in bcf_subset; force unpacking on VCF output
new e91d10b tbx: Allow indexing of empty files, do not segfault
new c9873a3 correct typos
new a7f24e2 deal with Number=A and Number=G INFO and FORMAT fields when trimming alleles
new a7f4597 add new tool vcfsubset
new c420b54 add tests for vcfsubset
new db1edf3 vcfutils: bcf_gt_type should not be declared as static
new 5da7aef vcf.[hc]: API to update FILTER column. BCF output not supported yet in this version
new 49f9e95 vcfmerge, vcfnorm: Append command and version string to VCF header
new 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.
new 3f76a40 Updated tests
new 8876289 Replace with samtools's ksort
new d30f1aa resolved test/check.chk conflict
new 72b5b28 vcfcheck: Changed output format of Ts/Tv
new 45be6fe vcffilter,gtcheck: Added sanity checks; Extended help message; Changed the order of columns on gtcheck output
new 4523040 plot-vcfcheck: Produce the overlap by AF graphs
new 1994af5 vcfsubset: New -i,-e options for general filter expressions. In this version, only QUAL and INFO columns are supported.
new e567ef0 Add klist.h, as used by samtools
new 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 "."
new 0c275f6 Maintain the same API regardless of -D BGZF_MT
new 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.
new efa9530 vcfcheck: Fixed a bug in initialization of frame-shift calculation; More detailed FS output
new 7a5992c vcfnorm: Removed two assertions to allow realignment of MNPs
new b267fb4 Expose bam_hdr_init() in the public API header
new 8496905 Avoid conflicting with samtools's bam_index()
new c3d530e vcffilter: Change in neighbourhood function in SOM training, seems more robust with respect to random seed
new 0670753 Merge branch 'for-samtools' into develop
new eedca8d Merge branch 'razf_sync' of https://github.com/mp15/htslib into develop
new 0fb04c2 Add Travis CI control file
new 348c5a1 Merge branch 'master' into develop
new e47feba vcf core lib, vcfsubset, vcfmerge: First step towards binary BCF output. Functional but probably buggy.
new dbcc082 Resolved vcfmerge.c merge conflict
new 3ecd0cb vcfsubset: Make --apply-filters consistent with other tools
new 779e243 Merge remote branch 'remotes/sm15-mod/develop' into develop
new bdb550f Move format specifications to sam-spec repository
new 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.
new cbc4478 Test with both Clang and GCC
new 3c4259c vcfcheck: re-enabled stats by QUAL
new 7508806 Merge branch 'develop' of github.com:samtools/htslib into develop
new 7413bed Deleted files which were moved to the new samtools/bcftools.git repository
new ad5ee37 Remaining application code also moving repository
new dd9c5a2 Lift library source to the top-level directory
new f455afd New non-recursive build infrastructure
new 6799348 Build shared libraries, add "make install" target
new 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)
new e79e112 Major overhaul of CRAM code (originally imported from Samtools/htlib branch, and further back from Staden Package io_lib).
new 6df8103 Merge branch 'develop' of https://github.com/samtools/htslib into develop
new 47b7241 Further removal of various unusued portions of Staden io_lib.
new 417fc59 Switch from modifying CFLAGS to CPPFLAGS so we can do "make CFLAGS=-g".
new fa5d1a1 Bug fix to handle blank headers in SAM files.
new 5500ef0 Bug fix to stop sam view from converting 'H' into 'Z' types.
new 016efd5 Use strtoul instead of strtol for XX:B:I tags so that integers >2.14 billion work.
new e25066b Better handling of unknown references.
new 0649ecb Bug fix to khash-ification of sam_hdr_add_lines
new 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).
new 1e6f3cf Added some synthetic SAM test data and a test perl script to trial conversion between SAM, BAM and CRAM. A work in progress.
new eeb41a7 Bug fix to khashification of process_one_read.
new 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.
new 956f45b bgzf.c: Check return status of bgzf_read_block in bgzf_useek to catch gzipped (as opposed to bgzipped) files.
new 13698ea Added tests/test_view
new 039620b Update khash.h from upstream sources
new 6d9e20e Update kstring.[ch] from upstream sources
new ab92989 Bug fix to handle blank headers in SAM files
new 4b8c9b5 Bug fix to stop sam view from converting 'H' into 'Z' types.
new 83a9bdd Use strtoul instead of strtol for XX:B:I tags so that integers >2.14 billion work.
new 8256ea8 Use strtoul() for other unsigned 'B' types too
new fcb9563 constify input parameter to faidx_fetch_seq
new 750f564 Use config.h for configuration options
new c2e9391 Replace HTS_VERSION with hts_version()
new 842b21c Actually $(NUMERIC_VERSION) is more generic
new 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.
new c485827 Resolved merge conflict in Makefile, merged.
new fb60f0c vcf.h: Reverted back to bcf_float_is_* macros as the inlined unions break vcfmerge code, found a solution with the original version.
new 9946dc7 Fix union-based type-punning buglet
new 1f9b3db Use static inline, not just inline
new 919fd54 Keep the makefile non-recursive
new 12c677b Add faidx (FASTA index) description man page
new f59d50f vcf.h: New bcf_get_info_* and bcf_get_format_* calls
new b68bfbf Merge branch 'develop' of github.com:samtools/htslib into develop
new aac4601 Alphabetise, fix whitespace [minor]
new 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.
new 8e00f34 Merge branch 'develop' of github.com:samtools/htslib into develop
new 14a22ef vcf: Make sure GT comes always first in bcf1_update_format; Do not loose last newline in vcf_hdr_read; Updated tests.
new 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
new 85ecdc2 Add buffered low-level input/output streams
new 1013c35 synced_reader,vcf: Big rewrite of synced reader to allow more flexible handling of regions and targets in future.
new 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.
new 70b088e Warn if hFILE function return statuses are ignored
new 009dfb7 Refactoring [minor]
new 2b9a9d2 Add hseek() and htell() test cases
new 99f05d3 Flush or discard the buffer in hseek()
new 441af2e Maintain our own hFILE offset within the stream
new cb5cacc kfunc: Moved the kt_fisher_exact test from the original bcftools into htslib
new fd086ed bgzf: Fixed typo in block_address calculation in bgzf_seek
new 60f315f synced_vcf_reader: new bcf_sr_get_line macro and fix in vcf/bcf index interator initialization
new a6e1c9f vcf: Minor bug fixes and API touches
new 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
new 1a7dae0 Add hdestroy_buffer() for use in hopen_*() cleaning up
new 3c3d80a BGZF worker threads do no I/O themselves
new f20bae1 Use hFILE underneath BGZF, and add bgzf_hopen()
new 655227b Add hfile*.[ch] to $(HTSLIB_ALL)
new c88645c Merge branch 'io' into develop
new 5750966 Fix vcf_sweep.h dependencies
new c371324 Also run our tests
new 5bbaed6 Fix typo [minor]
new 3fa19a7 Lift mallocing & freeing to the generic hFILE code
new a3dae45 vcf: prevent segfault when sample columns do not exist but FORMAT column does
new 25459e9 Merge branch 'develop' of github.com:samtools/htslib into develop
new c0a0035 Remove unneeded cast
new 78bb557 On Windows, call knet_win32_init before using knet
new 5a5fe13 Merge branch 'develop' of github.com:samtools/htslib into develop
new 4be3a31 Don't #include bgzf.h from other htslib headers
new 5e277dd synced_reader: Expanded docs - example of usage
new 799ed4a vcf: Support for string values in FORMAT; handling missing BCF_BT_CHAR values in bcf_fmt_array()
new c9734f7 VCF header parsing: Handle pathological cases where less-than and greater-than signs are used in place of double quotes
new e7a2de6 Change *_itr_next() to take htsFile*, not BGZF*
new aca31de vcf: Non-critical vcf_parse1() errors must not go unnoticed by vcf_write1(). Fixed offending \0\n added by bcf_hdr_subset()
new 663f12e Replace "void *fp" by a union of the file pointers
new 193ac2f Fix -Wc++-compat warning / C++ compilation error
new 29290bc Use hFILE instead of stdio for uncompressed output
new ac7844a Add bgzf_raw_read() and bgzf_raw_write()
new 9dfcc35 Merge branch 'io' into develop
new fd13d8c Fixes in targets/regions VCF synced reading, now regions work when streamed. Removed redundant get_fmt API calls
new 4352ff1 Minor docs comment added
new 1de141b Merge branch 'develop' of github.com:samtools/htslib into develop
new 5ec2456 bgzf: Added ad-hoc checks to all hfile calls to keep compiler happy
new d5bd42c Properly ignore hclose() in bgzf_[d]open functions
new b0312f8 bcf_index_build: Check return status of helper calls
new 67a9231 Merge branch 'develop' of github.com:samtools/htslib into develop
new f716f35 (io_lib r3438/7)
new 525c5bd (io_lib r3439)
new 70a227b (io_lib r3460)
new 95d7e53 (io_lib r3461 minus arithmetic coder & last_name experimental parts)
new 8a76b46 (io_lib r3467)
new 265e2e7 Silenced a "pointer targets in initialization differ in signedness" warning.
new b3dccc2 Merge branch develop of github.com/jkbonfield/htslib into cram
new c41394f Move cram/ directory to the top-level
new 159a498 Add makefile dependencies for cram code
new 7fe5680 Merge the CRAM test harness into current htslib
new fb94dac Build test_view with -pthread
new 616a0a5 Enable warnings only if -Wno-unused-result works
new 30cf9e9 (io_lib r3470) Fixed re-calling refs2id so it clears cached r->last; the pointer becomes invalid.
new bbd6647 synced_reader: Added support for alleles in targets files to select best matching line out of possibly duplicate VCF records.
new 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
new 26425fa Merge branch 'cram' into develop
new 7b85b13 Proper initialization in hts_readlines
new 2ea61c2 bcf_index_build: Check if the BCF is compressed
new e806853 Remove -Wc++-compat for the sake of the CRAM code
new 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!
new 037860b Add bam_endpos(const bam1_t *)
new bce13c4 vcf.c: Proper freeing of memory taken by dirty info/fmt tags when update routine called multiple times
new 59c317e New feature in bcf_synced_reader: negate the sample selection in bcf_sr_set_samples by exclamation mark
new a4736dc vcf.h: Add out of range check into bcf_idinfo_exists() as it always has to be checked elsewhere.
new 9f6f905 vcf.h: New API call: bcf_get_genotypes()
new aa50834 Disentangle CRAM header loopiness [minor]
new 07d5457 vcf.c: Call bcf_unpack() on user's behalf in all bcf1_get/update routines
new 35621c0 synced_reader: Fixed an off by one error in bcf_sr_next_line() to properly match target alleles
new 3f4ecdf vcf: Tidied up vcf.h, made API more consistent and extended documentation
new bc86c10 vcf module: Made the naming more consistent to avoid confusion about which of the vcf/bcf_* function variant to use.
new 95321be Merge branch 'bcftools+calling' into develop
new 23d64b8 Merge branch 'develop' of github.com:samtools/htslib into develop
new 43e8305 hfile: Removed accidently commited local change in blksize
new 1ee29f4 Add SAM and VCF man pages extracted from samtools.1
new 1c9239f Add BAM_FSUPPLEMENTARY flag bit
new 638083f Get rid of %ld compilaiton warnings
new cf02167 Return bytes >= 0x80 from hgetc() correctly
new d359060 Fixed CRAM to code with the 0x800 supplementary flag.
new 4294c7f Merge pull request #27 from jkbonfield/develop
new 10ef097 vcf: New bcf_hdr_printf() call
new b5f5f16 Added copyright notices.
new d3803f3 Fixed errors in copyright due to pasting the MRC one and forgetting to change the organisation name. Oops!
new ab5077b Merge branch 'bcftools+calling' into develop
new dc77561 Move cram_seek() from cram_index.c to cram_io.c
new 6416ebf Use hFILE underneath cram_fd, and add cram_dopen()
new a1e76ad vcf: Print a comprehensible error message if unsupported version of BCF is encountered
new 3b9ba8e hts_open(fname, "r") detects format by peeking at the input
new b02146d Merge branch 'io' into develop
new b92504a Tab, newline, etc are not control characters
new 65a3ed4 Require lowercase [rw] mode letters in bgzf_open() etc
new ba4e3fc Limit input hFILE buffers to 32K [temporary hack version]
new 1282758 Fix tbx_itr_next() when given a textual (is_kstream) htsFile
new 091f27e test.pl: fail if any tests fail
new d37f6df hts_open(fname, "r") now works in both cases; no need for "rb"
new 44fc956 Format detection: non-compressed binaries; is_compressed setting
new 7eb91ef bcf_sr_open_reader(): Auto-detect input file format
new 43586c9 The file type not necessary any more when opening synced reader
new c413e8a Merge branch 'develop' into bcftools+calling
new 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.
new e2e0a4b Reverted a fix of "chr:pos-pos" index queries, the original version now works.
new c83a9c0 Merge branch 'develop' of https://github.com/samtools/htslib into develop
new 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.)
new f149e78 Added prototype for cram_set_header()
new c7612be Fixed a couple complaints from clang.
new 18f6183 Handle erroneous modes with neither 'r' nor 'w'
new d80899b Merge CRAM copyright notices and data race fixes from jkbonfield
new b185d95 Fixed a bunch of code warnings produced by clang's static analyser.
new b3d93ad A couple more clang reported errors, which are duplicates of previous ones. I assume omitted before due to duplication.
new a3fd2b0 Merge branch 'develop' of https://github.com/samtools/htslib into develop
new 6fd937f Robustness improvements following fuzz testing. (See io_lib r3500).
new bebdfea Merge cram_set_header() from github.com/jkbonfield/htslib
new 941b400 Merge branch develop of github.com/jkbonfield/htslib
new 1b2bc6e Added decoding checks for the most obvious of sam parsing failures.
new 3f3758d Removed old comment from earlier code.
new 2402fc0 Add hts_set_fai_filename(); parse .fai in sam_hdr_read()
new 2591937 Remove now-unused fn_aux hts_open() parameter
new 3e18c41 Merge branch 'develop' of https://github.com/samtools/htslib into develop
new bef7597 Further fixing of auxiliary tag decoding.
new 1344221 Added the ability to do samtools index on a CRAM file.
new f010407 Reinstate distinct bgzf_check_EOF() status for seek failure
new 6561746 Compile cleanly without warnings with gcc 4.6.3
new 2b7806d Fixed return status checks of fread calls
new d1f589d bcf_gt_type can now, optionally, give the index of the 2nd alt allele for GT_HET_AA genotypes
new c16f20b Merge pull request #33 from sm15/develop
new f1d9f6f Merge branch 'develop' into bcftools+calling
new 69cf8a2 vcf: Support for regions in the form chr|chr:pos|chr:from-to|chr:from-
new 7e67a39 Listed copyright and license notices.
new ef70ad5 Draft package.
new e5b2ce0 Merge branch 'develop' into debian/unstable
new a9d9405 Documented cram/*, collated copyright notices for works under the MIT license.
new 2fc6f3b Do not build a htslib binary package: there is not htscmd program anymore.
new 9cef38d tbx: Sanity check if the file type meets the expectation, detect non-numeric fields
new 65450dd hts_idx: check return status of bgzf_read
new 19beee0 bcf reader: Fix in chr:pos type of regions
new ff10faf Add hclose_abruptly() for stack unwinding after errors
new 5b22605 synced reader: Support for BED regions/target files
new d038d8e Change hts_close() to return int (error indication)
new ae0de02 synced reader: regions and targets now support VCF; Fix for match_alleles by reverting 0-terminating chr modification
new 66c4f41 synced reader: Give a hint when tabix was used with wrong column indexes for regions/targets
new 69778ad Fix bgzf_write() for large (> 2GB) blocks
new c861097 Install in and from debian/tmp.
new f981604 Merge branch 'develop' into debian/unstable
new d131c15 Corrected paths.
new bd6afa8 Make the package multi-architecture.
new 1f0dec9 Align package name on soname.
new 64a155a Align package name on soname.
new 708a9cf Clean test directory before packaging it.
new 99fb99a Submitted ITP #729282 with the current package descriptions.
new f823fee Merge branch 'debian/unstable' of github.com:Debian/htslib into debian/unstable
new a8bc3b1 pileup: Detect non-recoverable errors and exit with proper status
new e6a750b Uses pristine-tar and may use git-buildpackage.
new 802bf74 Upstream tag 0.2.0_rc3.
new e870f95 Watch GitHub.
new 937513b Mangle the upstream name, so that the tarball has a correct version number.
new 223459a vcf: new APIs bcf_alleles2gt and bcf_gt2alleles; bcf_synced_reader: recognise compressed BED files
new 20b8bf5 Resolved merge conflicts
new 7994a4b Merge branch 'bcftools+calling' into develop
new 2f7c559 Empty symbols file, to be populated by Debhelper.
new 129889c fakeroot dh_makeshlibs | patch -p0
new 8f1d57c Removed minor number.
new 3a74341 Corrected length of lines.
new 7ffdf2a Make dh-exec files executables, since we are using the 1.0 source format.
new 0b49d2f Pass dpkg build flags.
new 07a47f6 Make libhts-dev depend on libhts0.
new 1f97dc0 Prospective VCS URLs (Alioth is currently down…).
new 00c7f03 htslib (0.2.0~rc3-1) unstable; urgency=low
new 420896b Override PACKAGE_VERSION to avoid tags with a slash in the name.
new 72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode.
new ba56a71 Merge branch 'develop' into debian/unstable
new 96badc4 Changelog for work in progress.
new 7a66c32 Updated symbols file.
new bc53b5d Merge cram_index_build() from github.com/jkbonfield/htslib
new 923191c l_qname is unsigned, so is always >= 0
new bb71572 Ensure r is clearly always initialised [minor]
new 4e4501c Use $(LDFLAGS) & $(LDLIBS) when linking shared objects
new d6e1ad0 Use the exact type in malloc(N * sizeof(TYPE*)) etc
new 13b445b Fix pointer arithmetic [minor]
new 06eeee1 Add HTS_NORETURN and annotate fail() as such
new be359b5 Merge remote-tracking branch 'upstream/develop' into debian/unstable
new 86fd29c Refreshed changelog after pulling new upstream tag.
new f3bd296 New upstream tag; no new copyright nor license statement.
new d870946 Adjusted substitution variables following dpkg's warnings.
new 79b5d4e Use the Debian as package version.
new b60c181 Updated the changelog.
new 9469458 Removed debug command accidentally introduced.
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