[med-svn] [htslib] branch master updated (1c631e9 -> f2af2ad)
Charles Plessy
plessy at moszumanska.debian.org
Sat Aug 16 09:20:27 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository htslib.
from 1c631e9 Merge branch 'lite'
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 6561746 Compile cleanly without warnings with gcc 4.6.3
adds 2b7806d Fixed return status checks of fread calls
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 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 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 20b8bf5 Resolved merge conflicts
adds 7994a4b Merge branch 'bcftools+calling' into develop
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 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 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 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
new f192318 vcf: Support for IDX BCF tag
new 0c084f2 vcf: Output . for missing INFO, FMT and samples
new 9029156 vcf.c: Fixed a renaming artifact, bcf_clear1 should be bcf_clear
new 9d6defa vcf: qual now set to missing on bcf_clear; Avoid warnings about type-punned pointers
new 997c519 Output VCFv4.2 header
new 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.
new 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).
new 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.
new 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.
new 1a39edb Add mfsteal to mFILE, and use it in cram_populate_ref.
new 34227f8 Added missing return code checks. Fixed 'x' mode of mfreopen.
new b5ccf9b Merge branch 'develop' into bcftools+calling
new 06208f2 Updated test
new ea4dbc6 add support for Number=R fields when trimming alleles
new cfdc6fd vcf: Make sure fileformat is added only once
new 78a6ef3 Merge branch 'develop' of git://github.com/samtools/htslib into feature/number_R
new 312add9 vcf: New bcf_get_info_string() wrapper
new f78d671 vcf: New API bcf_get_format_string()
new 2b801d7 add support for Number=R fields when trimming alleles
new 0caf597 Allow overriding default columns indexes in bcf_sr_regions_init
new c7c3ada vcf: new function bcf_remove_filter()
new 36a8ce9 Merge branch 'develop' into bcftools+calling
new 03f3fd7 Merge branch 'bcftools+calling' into develop
new 4855f43 vcf: fix in bcf_get_genotypes, sanity check too strict for GT
new b57379f vcf: Tip to workaround missing contig tags
new b2aab8b hts indexing: Allow arbitrary chromosomal order.
new 2d0423a vcf: New bcf_hdr_id2hrec() and bcf_hrec_format() functions
new 96132f4 vcf: New vcf_write_line() function
new 600acc3 synced_bcf_reader: New bcf_sr_seek() function
new e7ffc82 vcf: New bcf_translate() and bcf_hdr_combine() API
new 60c22d4 idx: Support for "." queries to retrieve all records
new 4622eaf vcf: New bcf_has_filter() API function
new 9dbf592 Fix hseek() return value test
new 2daf614 Make filename argument a *const* char pointer
new 650202c Strict matching of strings in bam_str2flag
new b729954 vcf: new experimental bcf_hdr_set_samples() for subsetting
new 0eb4c88 Merge branch 'bcftools+calling' into develop
new 68848e2 bcf_hdr_set_samples() recognise lists vs file names
new fd657c4 Store readrec function pointer within hts_itr_t
new a60ff3f Make search key arguments *const* char pointers
new a8be0b8 Write strcmp() comparisons comprehensibly
new f0fb825 Add basic test exercising bcf_itr_queryi and bcf_itr_querys
new 4d123f2 hts_itr_querys() calls hts_itr_query() via a function parameter
new 655edab Add sam_itr_*() dealing with BAM and CRAM iterators interchangeably
new 42152a6 synced_reader: Better handling of target alleles
new ad17bb8 bcf_sr_set_samples to use the new --sample convention
new fde4bd9 vcf: New bcf_get_info_flag() API
new a6cbed2 Added some EOF block creation and checking.
new ae92627 Bug fix to cram_next_slice(). The new while loop checking for non-empty blocks caused a crash when multi-threading.
new 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.
new 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.
new edb12c3 Merge branch 'develop' of https://github.com/samtools/htslib into develop
new 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.
new 939f6ea Merge branch 'develop' of https://github.com/samtools/htslib into develop
new 19ccc09 Fixed initialisation of CRAM indexing when the CRAM file contains refids that aren't sequential.
new 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.
new 843a063 Fixed the iterator to be 1-based inclusive coordinates for CRAM.
new 025ecb3 Also initialise tid in case user code looks at it
new 0e76a59 Merge pull request #46, CRAM EOF blocks
new bae6c41 vcf: Abort on broken VCFs with multiple/trailing spaces/tabs
new 0038f9e vcf: Don't let unpack_*_core forget the to-be-freed pointer
new c62982e hts_expand0: type ptr properly, it can be of different type
new 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.
new 322b28b Fixed EOF check. The usual code path had the correct check, but an empty cram triggered the incorrect code.
new dc45cfc Bug fix to the SAM header padding. It could go negative and then fail to write the header.
new 2279b3e Merge pull request #60, CRAM EOF block improvements
new 85b864f To avoid confusion, make bcf_get_*_int and bcf_update_*_int symetric
new aac5df5 hts_idx_load: Print warning when index is older than data
new 5e03160 Make synced reader aware of bcf_hdr_set_sample(), expanded docs
new 2eb509e Reduced the number of realloc calls zlib_mem_inflate(), while hopefully not overallocating much either.
new 728ad50 Merge pull request #62, minor CRAM updates
new d4d37c0 synced_reader: New bcf_sr_region_done macro
new 5a340a1 Check cram_eof() before calling cram_close()
new 39558ce bcf_translate: Catch unchecked errors
new c336894 More sensible Quals of matching bases in overlaps
new bcbfe37 Ignore operation-not-supported errors in fd_flush
new c38cf60 Keep the style of the surrounding code
new bdb6a4a Add HTS_IDX_NONE and document HTS_IDX_*
new f6c37a5 Fixes incorrect MD5 calculation in cram_write_SAM_hdr
new 21ca653 Merge #68, fix incorrect length given to MD5 calculation
new 3ea22a1 Add 'a' (append) mode letter; propagate mode letters
new 0d95c21 Add "data:blahblah" in-memory hFILE backend (read-only)
new cb7f6e9 fix remote fetching of regions for bam and vcf
new babaaf3 Use hFILE rather than knet in test_and_fetch()
new 1069b17 Merge #70, fetching of remote BAM/VCF indices
new 78e237b Fixed a bug when loading in fasta files consisting of all sequence on a single line and in lowercase.
new 5c65920 vcf: Allow omitted trailing FORMAT fields
new 692bb41 Fix sam_format1 failure on lines ending in integer/float tags and issue #63
new 30b4033 Rewrite __skip_tag() as skip_aux()
new ab84296 Add sam aux field tests
new 20df6b9 Merge sam_format1() and __skip_tag() fixes (PR #73)
new 5bdc06d synced_reader: Init position correctly
new c6f8531 Add ks_release() to kstring.h
new 321c402 Reinstate bam_header_dup as bam_hdr_dup
new fb23174 Fix typo in comment
new fee84e0 synced_reader: Init position correctly
new fca50b8 Merge branch 'develop' into bcftools+calling
new 1435a5d Merge branch 'develop' into bcftools+calling
new d91c9bb Merge branch 'bcftools+calling' into develop
new fe173b6 Make hfile.h part of the public API
new d7f0ae1 Add MIT/Expat license boilerplate
new 0180921 Define __attribute__ macros in a new (semi-public) header
new ec3a15a Fixed comment typo
new 22dedbe Merge pull request #79 from spalte/comment_typo
new cc207d8 hts_idx: fixed indexing of NO_COOR blocks
new cf693ad This resolves #49
new d66571e Propagate error codes for CRAM_OPT_RANGE
new 3490604 vcf: Propagate error in bcf_hdr_append
new 9d640ff Fixed off-by-one in bcf_get_format_values
new 9dec00e Construct HTS_IDX_REST and HTS_IDX_NONE iterators without an index
new b26a445 Propagate error from bcf_hdr_printf
new f7953db hts_readlist modifed to explicitly indicate file name vs list
new acfeb8a make sure we have found values for AC _and_ AN before using
new 5c80322 Merge pull request #82 from sm15/feature/bcf_calc_ac_bugfix
new 503c95a Support for =X cigars in mpileup overlaps.
new bb4721c faidx: Set error status if unknown seq is queried
new cd410e1 Add duplication function for the bam1_t interface
new 42d6aa1 Merge bam_dup1() addition (PR #80)
new 3e52ddb Migrate documentation from samtools bam.h to sam.h and add a few more items
new 128d97d bcf_hdr_subset: To allow sanity checks, mark missing samples
new 52ecc97 bcf_sr_seek to seek to start with seq=NULL
new eed28cb bcf_remove_alleles: Fix indexing range for Number=A alleles
new df2c538 Silence -Wstrict-prototypes warnings
new 388abc7 Fixed BCF output after bcf1_sync_alleles, simplified
new 4a5dcf4 bcf_remove_alleles to work with BCF output
new f5c96ca Added bgzip and tabix
new bd6ed8b .gitignore tabix and bgzip
new 20b6f6d Create trunk copy
new 8b14e7f Change copyright notices now that MIT has approved open source distribution.
new 4c42d43 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
new 0d51797 initial source code. It is BUGGY!
new 7d22a01 bgzip is more like gzip in its command-line interface
new dcd2f78 * tabix-0.0.0-1 (r500) * apparently working
new e0afbb5 * tabix-0.0.0-2 (r501) * accelerate ti_readline()
new 0f56c58 * tabix-0.0.0-3 (r502) * support meta lines (not tested) * I am going to make the index file in the BGZF format
new 05df526 * tabix-0.0.0-4 (r503) * index files are bgzf compressed
new 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
new 446b6e4 documentation
new f667bfc Release tabix-0.1.0
new a2d85ec Release tabix-0.1.1
new 81170d8 * tabix-0.1.3 (r543) * fixed another off-by-one bug
new f79c886 removed a line of debugging code
new 15159c7 Added the -l option for listing chromosomes
new ac9fc9f Fix in src/dst file detection and slight change of behaviour
new 7cacea8 The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
new 79d6239 * added the format specification * fixed a typo in bgzip
new 4fb1b67 * tabix-0.1.3-2 (r555) * do not overwrite index file by default * a little code cleanup
new 9b14f2c * tabix-0.1.3-3 (r556) * fixed a small memory leak in knetfile * fixed a minor bug for remote downloading
new 9f16a45 Release tabix-0.1.4 (r559)
new 50f5b5c * Release tabix-0.1.5 (r560) * Improve seeking efficiency. Index file needs to be rebuilt.
new cf389c2 If nothing bad happens, this will become 0.1.6
new c6770bb Release tabix-0.1.6
new 6fa709d * improved C/Perl APIs * added test for Perl * added an tiny example
new bccdc09 Release tabix-0.2.0
new a79e73a Release tabix-0.2.1
new a39b546 Release tabix-0.2.2
new 31c8bd3 Complain about not-bgzipped files and check for noncontinuous chromosome blocks
new 07f01ed Fix: Exit with an error rather than segfault when index is not present and region is queried
new 3c60871 fixed a bug in C/Java when n_off == 0
new 128523b patches by Peter Chines
new 2c0b7ee Added -h option to print header lines
new 4a6e786 Disable "unknown target name or minus interval" warning.
new bbcc0b2 Release tabix-0.2.3
new 08d08a2 Prevent the common user mistake and check the timestamps of the vcf and index file
new 4dedb83 Fix: Complain only when VCF is newer, not newer or same mtime
new 1cdcb39 New -r (reheader) option for efficient header replacement.
new 7d48a19 BED support
new 70e9ba8 update to the latest bgzf.*
new 87f69fe fixed two bugs due to recent changes
new e4477ce update version number
new 046c761 Release tabix-0.2.4 (r949)
new bec709b Release tabix-0.2.5 (r964)
new 8ff4c17 Querying remote files required -f option on some systems
new 83afb06 updated BGZF
new 46b2463 Added option for printing header lines only
new c2a5899 Guess the filetype from the file extension when -p not given
new 8abdff6 Assume GFF format when the file type cannot be guessed, as in the previous version
new a33c73e Even better, do this only for reading
new 1344d39 Fix: allow custom formats
new f14716c More informative error message about missing or out-of-date tabix index
new 8af2d0a Fix: do not drop first record with both -B and -h
new a09bef9 -C to output lines not overlapping BED
new c49a4ec bgzip now compiles
new cf03c20 Use htslib's bgzf.h, faidx.h, and razf.h
new 90ae62f Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
new 716070d tview and bgzip: Check that the files are bgzipped, not gzipped.
new 5c1e1bb bgzip: Do not overwrite input files when -b or -s are given
new 0f9a088 Check return status of IO calls to prevent gcc 4.6.3 warnings
new ec581d6 Merge tabix and samtools bgzip.c and tabix.c
new 1d963d7 Initial version of bgzip and tabix with htslib.
new f38b5e2 Merge bgzip.c and tabix.c/.1 history from github.com/samtools/tabix
new e45b3f3 Fix bgzip and tabix dependencies and link commands
new 35f4642 Exit statuses are non-negative
new 5adb883 bcf_subset: Reset n_fmt fields when all samples are dropped
new 6e2ebc4 synced_reader: Regions operate on two as well as three columns again
new db8055a bcf1_sync: Update rlen for new records as well
new 41e8793 Merge branch 'bcftools+calling' into develop
new 104adb5 Silence -Wstrict-prototypes warning
new 996b3c0 Check sam_open() and sam_close() return values
new 1ce5791 bcf_write: sanity check the number of samples, resolves #55
new 9ed346d Return "" from bam_flag2str(0) rather than NULL
new e321182 Bug fix to CRAM indexing and index usage.
new d3bf5b6 Fixed two small memory leaks.
new 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.
new eb71ced Better fix for container memory leak.
new 0557506 Merge CRAM indexing bug fixes (PR #85)
new 5003f7b Add hts_set_threads() file I/O threading API
new 70be28c Fix bgzf_write() and bgzf_flush_try() error handling
new f99d5ba Fix bam_write1() error handling
new a1fb3bd vcf_parse: Detect missing INFO values in vectors
new f1f2950 Merge branch 'develop' into bcftools+calling
new 9db893a For bcftools to work with CSI indexes up to 2^31-1
new fc4a18b New bcf_hdr_[sg]et_version API; bcf_hdr_subset preserves VCF version
new 8deb11d Merge branch 'bcftools+calling' into develop
new dc9a0fe bgzf: Support for reading gzip-compressed files.
new dd58092 Minor comment change
new 02721b7 bgzf: Support for FCOMMENT gzip header
new 165850e bgzf: Support the remaining optional GZIP header fields
new 2cc7ea4 bcf_sr: New missed_reg_handler and bcf_sr_regions_flush() function
new d49dfa6 vcf: New bcf_dup() function
new 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.
new e76b489 idx: Don't create broken .tbi or .csi when file unsorted (VCF/BCF/BAM)
new 8d283ed Sanitised the setting of fd->empty_container into one place. This also fixes the samtools bug #146.
new 7d11028 Fix forgotten s/razip/bgzip/
new b3a7868 Remove RAZF source code
new e7bd15c Check CIGAR string has fewer than 2^16 operators
new 7e059de Add a comment to deobfuscate bam_cigar_type
new b62e668 Fix "unrecognized CIGAR operator" diagnostic
new 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.
new 6622a18 Add functions for idxstats
new 885bba0 Improve hts_idx_get_stat to work for more file types
new 416f02a Return 0/-1 rather than bool; parenthesise C macro
new d3ec3e2 Merge API functions for index statistics (PR #83)
new 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.
new 0c360be Check index file magic numbers and I/O
new e8806c7 Fix endianness problems outwith CRAM code
new 49610fc Set NM/MD creation to be on by default.
new 97c1e18 synced_reader: Removed unused code
new aa68a05 vcf: Change of bcf_hdr_add_sample() usage.
new 252d27d Add sam_open_mode() API function
new 7d61caf Remove val_unused -- use HTS_UNUSED instead
new 53c3ba8 bcf_write: Error message instead of assert + propagate the error up
new 6a5b9fd vcf_parse: Detect incorrect number of columns
new 6172a08 vcf: Fix BCF syncing when only partially unpacked
new 3cdd62f vcf: Fixes in bcf_translate
new 0d4e155 bgzf: Do not end prematurely on non-critical Z_BUF_ERROR zlib error
new c8c5b31 vcf: Fix bcf_hdr_id2hrec, col_type parameter is needed as well
new aff3226 bcf_trim_als: Propagate error instead of assert
new 9074f89 bcf_update_alleles: Reference length with INFO/END
new a969d0f Fix in index initialization
new 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 [...]
new 3b87c0e Improved bug fix of bcf1_sync() from the commit 2504243:
new 049f877 synced_reader: Consider non-variant sites as matching in comparisons
new c158790 Add extern "C" around API to enable C++ linking
new 5f406e5 Merge pull request #108 from MauricioCarneiro/develop
new eb27d19 vcf: Detect broken structured header lines
new 7d31af0 synced_reader: Logical complements of target regions
new 663b9cf bgzf: Translate windows line endings
new 56d740e bcf_hdr_combine: Check for tags of conflicting lengths
new 642783e faidx: Exit with an error if run on gzip-ed files
new cc23df1 Fixed REF_PATH to handle URLs better.
new 42775eb Suppress compression suffix search on default EBI MD5 service
new b7c2a46 Merge REF_PATH fixes and libcurl removal (PR #111)
new fcd0bd8 vcf: Support for mpileup's symbolic <X> allele
new 894ebcf On open failure, set errno instead of printing message
new 5498c0a Expose bcf_hdr_parse
new ac4f30f vcf: Expose bcf_hdr_sync() and hrec_add_idx()
new e12c343 vcf: bcf_hdr_get_hrec() interface made more general
new b039db8 mpileup: Support for cigar operator "P"
new 51d9560 faidx: new faidx_has_seq() call
new 17d3d47 faidx: Fixed copy-and-paste documentation error
new 399b580 hts_file_type: correct return of FT_VCF_GZ
new dedd405 Merge pull request #113 from mcshane/feature/hts_file_type_fix
new 232b77b Don't call freeaddrinfo() when getaddrinfo() fails
new 4b024e1 Bug fix in bcf_trim_alleles()
new c95dbc5 mpileup: Support for cigar operation N
new dde9bdb Rationalise include guard macro names
new 949d267 Ensure installation directories are world-executable
new 19b5a8e Omit control files and README.md from release tarballs
new 7dcaf17 Add license file
new 45aaa8b Add MIT/Expat license boilerplate
new 8b17b24 Fix copy/pasto
new aaf99a9 Files under cram/ are BSD-licensed
new deecae2 Add copyright notices and licensing boilerplate
new 8bb77cc Add klib copyright notices and licensing boilerplate
new cf35bd6 Add copyright notices and licensing boilerplate
new b61c691 Add copyright notices and licensing boilerplate
new 5cb1182 Update copyright notices to reflect historic changes
new 0b6597c Add copyright notices and licensing boilerplate
new 9155cca Update copyright years to reflect historic changes
new d9122b7 Add copyright notices and licensing boilerplate
new b5fbf05 Add copyright notices and licensing boilerplate
new 7d3c063 Add copyright notices and licensing boilerplate
new f19ff09 Add copyright notices and licensing boilerplate
new 61ad3a6 Add copyright notices and licensing boilerplate
new 9fc07d5 Merge copyright notice and licensing boilerplate additions
new e770a1b Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
new 9e95d31 Link shared library against libm and libpthread
new 64bebbb Create a pkg-config description for easy linking
new c99ed6a bgzf_seek: Assign corect block_address (on behalf of Chris Smowton)
new 0b0736a Add basic INSTALL and README files
new f2af2ad Release 1.0: first released HTSlib package
The 302 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitattributes | 4 +
.gitignore | 25 +-
.travis.yml | 8 +
INSTALL | 25 +
LICENSE | 69 +
Makefile | 350 +-
README | 5 +
README.md | 29 +-
abreak.c | 197 -
bam2bed.c | 64 -
bam2fq.c | 116 -
bamidx.c | 20 -
bamshuf.c | 141 -
bcfidx.c | 17 -
bgzf.c | 1089 ++
bgzip.c | 284 +
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 | 503 +
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 | 357 +
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 +
doc/.gitignore | 32 -
doc/BCFv2.tex | 95 -
doc/index.tex | 64 -
faidx.5 | 147 +
faidx.c | 463 +
hfile.c | 526 +
hfile_internal.h | 75 +
hfile_net.c | 99 +
hts.c | 1360 +++
htslib.mk | 144 +
htslib.pc.in | 10 +
htslib/Makefile | 31 -
htslib/bgzf.c | 710 --
htslib/bgzf.h | 403 +-
htslib/faidx.c | 437 -
htslib/faidx.h | 133 +-
htslib/hfile.h | 204 +
htslib/hts.c | 920 --
htslib/hts.h | 287 +-
htslib/hts_defs.h | 47 +
htslib/kfunc.h | 75 +
htslib/khash.h | 161 +-
htslib/khash_str2int.h | 122 +
htslib/klist.h | 121 +
htslib/knetfile.h | 26 +
htslib/kseq.h | 5 +
htslib/ksort.h | 157 +-
htslib/kstdint.h | 64 -
htslib/kstring.h | 183 +-
htslib/razf.c | 853 --
htslib/razf.h | 134 -
htslib/sam.c | 1205 --
htslib/sam.h | 386 +-
htslib/synced_bcf_reader.c | 809 --
htslib/synced_bcf_reader.h | 298 +-
htslib/tbx.c | 264 -
htslib/tbx.h | 68 +-
htslib/vcf.c | 1559 ---
htslib/vcf.h | 961 +-
htslib/vcf_sweep.h | 39 +
htslib/vcfutils.c | 257 -
htslib/vcfutils.h | 77 +-
htslib_vars.mk | 38 +
kfunc.c | 280 +
htslib/knetfile.c => knetfile.c | 24 +-
kstring.c | 254 +
main.c | 224 -
misc/plot-vcfcheck | 1579 ---
sam.5 | 68 +
sam.c | 1822 +++
samview.c | 70 -
synced_bcf_reader.c | 1215 ++
tabix.1 | 155 +
tabix.c | 467 +-
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/check.chk | 60 -
test/check.vcf | 37 -
test/compare_sam.pl | 172 +
test/ex1.gtf.gz | Bin 3778 -> 0 bytes
test/ex3.sam | 14 -
test/fieldarith.c | 72 +
test/fieldarith.sam | 15 +
test/hfile.c | 204 +
test/isec.a.vcf | 27 -
test/isec.ab.C.out | 3 -
test/isec.ab.any.out | 7 -
test/isec.ab.both.out | 8 -
test/isec.ab.out | 3 -
test/isec.b.vcf | 27 -
test/isec.tab | 5 -
test/isec.tab.out | 28 -
test/merge.a.chk | 58 -
test/merge.a.vcf | 33 -
test/merge.abc.out | 44 -
test/merge.b.vcf | 29 -
test/merge.c.vcf | 31 -
test/norm.fa | 18 -
test/norm.fa.fai | 3 -
test/norm.out | 19 -
test/norm.vcf | 18 -
test/query.out | 12 -
test/query.vcf | 31 -
test/sam.c | 143 +
test/tabix.2.3199812.out | 1 -
test/test-vcf-api.c | 235 +
test/{ex2.vcf => test-vcf-api.out} | 23 +-
test/test-vcf-sweep.c | 112 +
test/test-vcf-sweep.out | 4 +
test/test.pl | 144 +-
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 +
vcf.5 | 120 +
vcf.c | 3133 ++++++
vcf_sweep.c | 182 +
vcfcheck.c | 802 --
vcffilter.c | 1243 ---
vcfgtcheck.c | 587 -
vcfisec.c | 387 -
vcfmerge.c | 1097 --
vcfnorm.c | 648 --
vcfquery.c | 703 --
vcfutils.c | 666 ++
vcfview.c | 107 -
189 files changed, 57466 insertions(+), 17035 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .travis.yml
create mode 100644 INSTALL
create mode 100644 LICENSE
create mode 100644 README
delete mode 100644 abreak.c
delete mode 100644 bam2bed.c
delete mode 100644 bam2fq.c
delete mode 100644 bamidx.c
delete mode 100644 bamshuf.c
delete mode 100644 bcfidx.c
create mode 100644 bgzf.c
create mode 100644 bgzip.c
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
delete mode 100644 doc/.gitignore
delete mode 100644 doc/BCFv2.tex
delete mode 100644 doc/index.tex
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
delete mode 100644 htslib/Makefile
delete mode 100644 htslib/bgzf.c
delete mode 100644 htslib/faidx.c
create mode 100644 htslib/hfile.h
delete mode 100644 htslib/hts.c
create mode 100644 htslib/hts_defs.h
create mode 100644 htslib/kfunc.h
create mode 100644 htslib/khash_str2int.h
create mode 100644 htslib/klist.h
delete mode 100644 htslib/kstdint.h
delete mode 100644 htslib/razf.c
delete mode 100644 htslib/razf.h
delete mode 100644 htslib/sam.c
delete mode 100644 htslib/synced_bcf_reader.c
delete mode 100644 htslib/tbx.c
delete mode 100644 htslib/vcf.c
create mode 100644 htslib/vcf_sweep.h
delete mode 100644 htslib/vcfutils.c
create mode 100644 htslib_vars.mk
create mode 100644 kfunc.c
rename htslib/knetfile.c => knetfile.c (96%)
create mode 100644 kstring.c
delete mode 100644 main.c
delete mode 100755 misc/plot-vcfcheck
create mode 100644 sam.5
create mode 100644 sam.c
delete mode 100644 samview.c
create mode 100644 synced_bcf_reader.c
create mode 100644 tabix.1
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
delete mode 100644 test/check.chk
delete mode 100644 test/check.vcf
create mode 100755 test/compare_sam.pl
delete mode 100644 test/ex1.gtf.gz
delete mode 100644 test/ex3.sam
create mode 100644 test/fieldarith.c
create mode 100644 test/fieldarith.sam
create mode 100644 test/hfile.c
delete mode 100644 test/isec.a.vcf
delete mode 100644 test/isec.ab.C.out
delete mode 100644 test/isec.ab.any.out
delete mode 100644 test/isec.ab.both.out
delete mode 100644 test/isec.ab.out
delete mode 100644 test/isec.b.vcf
delete mode 100644 test/isec.tab
delete mode 100644 test/isec.tab.out
delete mode 100644 test/merge.a.chk
delete mode 100644 test/merge.a.vcf
delete mode 100644 test/merge.abc.out
delete mode 100644 test/merge.b.vcf
delete mode 100644 test/merge.c.vcf
delete mode 100644 test/norm.fa
delete mode 100644 test/norm.fa.fai
delete mode 100644 test/norm.out
delete mode 100644 test/norm.vcf
delete mode 100644 test/query.out
delete mode 100644 test/query.vcf
create mode 100644 test/sam.c
delete mode 100644 test/tabix.2.3199812.out
create mode 100644 test/test-vcf-api.c
rename test/{ex2.vcf => test-vcf-api.out} (51%)
create mode 100644 test/test-vcf-sweep.c
create mode 100644 test/test-vcf-sweep.out
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
create mode 100644 vcf.5
create mode 100644 vcf.c
create mode 100644 vcf_sweep.c
delete mode 100644 vcfcheck.c
delete mode 100644 vcffilter.c
delete mode 100644 vcfgtcheck.c
delete mode 100644 vcfisec.c
delete mode 100644 vcfmerge.c
delete mode 100644 vcfnorm.c
delete mode 100644 vcfquery.c
create mode 100644 vcfutils.c
delete mode 100644 vcfview.c
--
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