[med-svn] [htslib] branch master updated (9469458 -> 1c631e9)
Charles Plessy
plessy at moszumanska.debian.org
Fri Nov 22 04:56:39 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository htslib.
omits 9469458 Removed debug command accidentally introduced.
omits b60c181 Updated the changelog.
omits 79b5d4e Use the Debian as package version.
omits d870946 Adjusted substitution variables following dpkg's warnings.
omits f3bd296 New upstream tag; no new copyright nor license statement.
omits 86fd29c Refreshed changelog after pulling new upstream tag.
omits be359b5 Merge remote-tracking branch 'upstream/develop' into debian/unstable
omits 06eeee1 Add HTS_NORETURN and annotate fail() as such
omits 13b445b Fix pointer arithmetic [minor]
omits d6e1ad0 Use the exact type in malloc(N * sizeof(TYPE*)) etc
omits 4e4501c Use $(LDFLAGS) & $(LDLIBS) when linking shared objects
omits bb71572 Ensure r is clearly always initialised [minor]
omits 923191c l_qname is unsigned, so is always >= 0
omits bc53b5d Merge cram_index_build() from github.com/jkbonfield/htslib
omits 7a66c32 Updated symbols file.
omits 96badc4 Changelog for work in progress.
omits ba56a71 Merge branch 'develop' into debian/unstable
omits 72b5c4a Finally use the 3.0 (quilt) format in single-debian-patch mode.
omits 420896b Override PACKAGE_VERSION to avoid tags with a slash in the name.
omits 00c7f03 htslib (0.2.0~rc3-1) unstable; urgency=low
omits 1f97dc0 Prospective VCS URLs (Alioth is currently down…).
omits 07a47f6 Make libhts-dev depend on libhts0.
omits 0b49d2f Pass dpkg build flags.
omits 7ffdf2a Make dh-exec files executables, since we are using the 1.0 source format.
omits 3a74341 Corrected length of lines.
omits 8f1d57c Removed minor number.
omits 129889c fakeroot dh_makeshlibs | patch -p0
omits 2f7c559 Empty symbols file, to be populated by Debhelper.
omits 7994a4b Merge branch 'bcftools+calling' into develop
omits 20b8bf5 Resolved merge conflicts
omits 223459a vcf: new APIs bcf_alleles2gt and bcf_gt2alleles; bcf_synced_reader: recognise compressed BED files
omits 937513b Mangle the upstream name, so that the tarball has a correct version number.
omits e870f95 Watch GitHub.
omits 802bf74 Upstream tag 0.2.0_rc3.
omits e6a750b Uses pristine-tar and may use git-buildpackage.
omits a8bc3b1 pileup: Detect non-recoverable errors and exit with proper status
omits f823fee Merge branch 'debian/unstable' of github.com:Debian/htslib into debian/unstable
omits 99fb99a Submitted ITP #729282 with the current package descriptions.
omits 708a9cf Clean test directory before packaging it.
omits 64a155a Align package name on soname.
omits 1f0dec9 Align package name on soname.
omits bd6afa8 Make the package multi-architecture.
omits d131c15 Corrected paths.
omits f981604 Merge branch 'develop' into debian/unstable
omits c861097 Install in and from debian/tmp.
omits 69778ad Fix bgzf_write() for large (> 2GB) blocks
omits 66c4f41 synced reader: Give a hint when tabix was used with wrong column indexes for regions/targets
omits ae0de02 synced reader: regions and targets now support VCF; Fix for match_alleles by reverting 0-terminating chr modification
omits d038d8e Change hts_close() to return int (error indication)
omits 5b22605 synced reader: Support for BED regions/target files
omits ff10faf Add hclose_abruptly() for stack unwinding after errors
omits 19beee0 bcf reader: Fix in chr:pos type of regions
omits 65450dd hts_idx: check return status of bgzf_read
omits 9cef38d tbx: Sanity check if the file type meets the expectation, detect non-numeric fields
omits 2fc6f3b Do not build a htslib binary package: there is not htscmd program anymore.
omits a9d9405 Documented cram/*, collated copyright notices for works under the MIT license.
omits e5b2ce0 Merge branch 'develop' into debian/unstable
omits ef70ad5 Draft package.
omits 7e67a39 Listed copyright and license notices.
omits 69cf8a2 vcf: Support for regions in the form chr|chr:pos|chr:from-to|chr:from-
omits f1d9f6f Merge branch 'develop' into bcftools+calling
omits c16f20b Merge pull request #33 from sm15/develop
omits d1f589d bcf_gt_type can now, optionally, give the index of the 2nd alt allele for GT_HET_AA genotypes
omits 2b7806d Fixed return status checks of fread calls
omits 6561746 Compile cleanly without warnings with gcc 4.6.3
omits f010407 Reinstate distinct bgzf_check_EOF() status for seek failure
omits 1344221 Added the ability to do samtools index on a CRAM file.
omits bef7597 Further fixing of auxiliary tag decoding.
omits 3e18c41 Merge branch 'develop' of https://github.com/samtools/htslib into develop
omits 2591937 Remove now-unused fn_aux hts_open() parameter
omits 2402fc0 Add hts_set_fai_filename(); parse .fai in sam_hdr_read()
omits 3f3758d Removed old comment from earlier code.
omits 1b2bc6e Added decoding checks for the most obvious of sam parsing failures.
omits 941b400 Merge branch develop of github.com/jkbonfield/htslib
omits bebdfea Merge cram_set_header() from github.com/jkbonfield/htslib
omits 6fd937f Robustness improvements following fuzz testing. (See io_lib r3500).
omits a3fd2b0 Merge branch 'develop' of https://github.com/samtools/htslib into develop
omits b3d93ad A couple more clang reported errors, which are duplicates of previous ones. I assume omitted before due to duplication.
omits b185d95 Fixed a bunch of code warnings produced by clang's static analyser.
omits d80899b Merge CRAM copyright notices and data race fixes from jkbonfield
omits 18f6183 Handle erroneous modes with neither 'r' nor 'w'
omits c7612be Fixed a couple complaints from clang.
omits f149e78 Added prototype for cram_set_header()
omits 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.)
omits c83a9c0 Merge branch 'develop' of https://github.com/samtools/htslib into develop
omits e2e0a4b Reverted a fix of "chr:pos-pos" index queries, the original version now works.
omits 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.
omits c413e8a Merge branch 'develop' into bcftools+calling
omits 43586c9 The file type not necessary any more when opening synced reader
omits 7eb91ef bcf_sr_open_reader(): Auto-detect input file format
omits 44fc956 Format detection: non-compressed binaries; is_compressed setting
omits d37f6df hts_open(fname, "r") now works in both cases; no need for "rb"
omits 091f27e test.pl: fail if any tests fail
omits 1282758 Fix tbx_itr_next() when given a textual (is_kstream) htsFile
omits ba4e3fc Limit input hFILE buffers to 32K [temporary hack version]
omits 65a3ed4 Require lowercase [rw] mode letters in bgzf_open() etc
omits b92504a Tab, newline, etc are not control characters
omits b02146d Merge branch 'io' into develop
omits 3b9ba8e hts_open(fname, "r") detects format by peeking at the input
omits a1e76ad vcf: Print a comprehensible error message if unsupported version of BCF is encountered
omits 6416ebf Use hFILE underneath cram_fd, and add cram_dopen()
omits dc77561 Move cram_seek() from cram_index.c to cram_io.c
omits ab5077b Merge branch 'bcftools+calling' into develop
omits d3803f3 Fixed errors in copyright due to pasting the MRC one and forgetting to change the organisation name. Oops!
omits b5f5f16 Added copyright notices.
omits 10ef097 vcf: New bcf_hdr_printf() call
omits 4294c7f Merge pull request #27 from jkbonfield/develop
omits d359060 Fixed CRAM to code with the 0x800 supplementary flag.
omits cf02167 Return bytes >= 0x80 from hgetc() correctly
omits 638083f Get rid of %ld compilaiton warnings
omits 1c9239f Add BAM_FSUPPLEMENTARY flag bit
omits 1ee29f4 Add SAM and VCF man pages extracted from samtools.1
omits 43e8305 hfile: Removed accidently commited local change in blksize
omits 23d64b8 Merge branch 'develop' of github.com:samtools/htslib into develop
omits 95321be Merge branch 'bcftools+calling' into develop
omits bc86c10 vcf module: Made the naming more consistent to avoid confusion about which of the vcf/bcf_* function variant to use.
omits 3f4ecdf vcf: Tidied up vcf.h, made API more consistent and extended documentation
omits 35621c0 synced_reader: Fixed an off by one error in bcf_sr_next_line() to properly match target alleles
omits 07d5457 vcf.c: Call bcf_unpack() on user's behalf in all bcf1_get/update routines
omits aa50834 Disentangle CRAM header loopiness [minor]
omits 9f6f905 vcf.h: New API call: bcf_get_genotypes()
omits a4736dc vcf.h: Add out of range check into bcf_idinfo_exists() as it always has to be checked elsewhere.
omits 59c317e New feature in bcf_synced_reader: negate the sample selection in bcf_sr_set_samples by exclamation mark
omits bce13c4 vcf.c: Proper freeing of memory taken by dirty info/fmt tags when update routine called multiple times
omits 037860b Add bam_endpos(const bam1_t *)
omits 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!
omits e806853 Remove -Wc++-compat for the sake of the CRAM code
omits 2ea61c2 bcf_index_build: Check if the BCF is compressed
omits 7b85b13 Proper initialization in hts_readlines
omits 26425fa Merge branch 'cram' into develop
omits 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
omits bbd6647 synced_reader: Added support for alleles in targets files to select best matching line out of possibly duplicate VCF records.
omits 30cf9e9 (io_lib r3470) Fixed re-calling refs2id so it clears cached r->last; the pointer becomes invalid.
omits 616a0a5 Enable warnings only if -Wno-unused-result works
omits fb94dac Build test_view with -pthread
omits 7fe5680 Merge the CRAM test harness into current htslib
omits 159a498 Add makefile dependencies for cram code
omits c41394f Move cram/ directory to the top-level
omits b3dccc2 Merge branch develop of github.com/jkbonfield/htslib into cram
omits 265e2e7 Silenced a "pointer targets in initialization differ in signedness" warning.
omits 8a76b46 (io_lib r3467)
omits 95d7e53 (io_lib r3461 minus arithmetic coder & last_name experimental parts)
omits 70a227b (io_lib r3460)
omits 525c5bd (io_lib r3439)
omits f716f35 (io_lib r3438/7)
omits 67a9231 Merge branch 'develop' of github.com:samtools/htslib into develop
omits b0312f8 bcf_index_build: Check return status of helper calls
omits d5bd42c Properly ignore hclose() in bgzf_[d]open functions
omits 5ec2456 bgzf: Added ad-hoc checks to all hfile calls to keep compiler happy
omits 1de141b Merge branch 'develop' of github.com:samtools/htslib into develop
omits 4352ff1 Minor docs comment added
omits fd13d8c Fixes in targets/regions VCF synced reading, now regions work when streamed. Removed redundant get_fmt API calls
omits 9dfcc35 Merge branch 'io' into develop
omits ac7844a Add bgzf_raw_read() and bgzf_raw_write()
omits 29290bc Use hFILE instead of stdio for uncompressed output
omits 193ac2f Fix -Wc++-compat warning / C++ compilation error
omits 663f12e Replace "void *fp" by a union of the file pointers
omits aca31de vcf: Non-critical vcf_parse1() errors must not go unnoticed by vcf_write1(). Fixed offending \0\n added by bcf_hdr_subset()
omits e7a2de6 Change *_itr_next() to take htsFile*, not BGZF*
omits c9734f7 VCF header parsing: Handle pathological cases where less-than and greater-than signs are used in place of double quotes
omits 799ed4a vcf: Support for string values in FORMAT; handling missing BCF_BT_CHAR values in bcf_fmt_array()
omits 5e277dd synced_reader: Expanded docs - example of usage
omits 4be3a31 Don't #include bgzf.h from other htslib headers
omits 5a5fe13 Merge branch 'develop' of github.com:samtools/htslib into develop
omits 78bb557 On Windows, call knet_win32_init before using knet
omits c0a0035 Remove unneeded cast
omits 25459e9 Merge branch 'develop' of github.com:samtools/htslib into develop
omits a3dae45 vcf: prevent segfault when sample columns do not exist but FORMAT column does
omits 3fa19a7 Lift mallocing & freeing to the generic hFILE code
omits 5bbaed6 Fix typo [minor]
omits c371324 Also run our tests
omits 5750966 Fix vcf_sweep.h dependencies
omits c88645c Merge branch 'io' into develop
omits 655227b Add hfile*.[ch] to $(HTSLIB_ALL)
omits f20bae1 Use hFILE underneath BGZF, and add bgzf_hopen()
omits 3c3d80a BGZF worker threads do no I/O themselves
omits 1a7dae0 Add hdestroy_buffer() for use in hopen_*() cleaning up
omits 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
omits a6e1c9f vcf: Minor bug fixes and API touches
omits 60f315f synced_vcf_reader: new bcf_sr_get_line macro and fix in vcf/bcf index interator initialization
omits fd086ed bgzf: Fixed typo in block_address calculation in bgzf_seek
omits cb5cacc kfunc: Moved the kt_fisher_exact test from the original bcftools into htslib
omits 441af2e Maintain our own hFILE offset within the stream
omits 99f05d3 Flush or discard the buffer in hseek()
omits 2b9a9d2 Add hseek() and htell() test cases
omits 009dfb7 Refactoring [minor]
omits 70b088e Warn if hFILE function return statuses are ignored
omits 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.
omits 1013c35 synced_reader,vcf: Big rewrite of synced reader to allow more flexible handling of regions and targets in future.
omits 85ecdc2 Add buffered low-level input/output streams
omits 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
omits 14a22ef vcf: Make sure GT comes always first in bcf1_update_format; Do not loose last newline in vcf_hdr_read; Updated tests.
omits 8e00f34 Merge branch 'develop' of github.com:samtools/htslib into develop
omits 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.
omits aac4601 Alphabetise, fix whitespace [minor]
omits b68bfbf Merge branch 'develop' of github.com:samtools/htslib into develop
omits f59d50f vcf.h: New bcf_get_info_* and bcf_get_format_* calls
omits 12c677b Add faidx (FASTA index) description man page
omits 919fd54 Keep the makefile non-recursive
omits 1f9b3db Use static inline, not just inline
omits 9946dc7 Fix union-based type-punning buglet
omits fb60f0c vcf.h: Reverted back to bcf_float_is_* macros as the inlined unions break vcfmerge code, found a solution with the original version.
omits c485827 Resolved merge conflict in Makefile, merged.
omits 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.
omits 842b21c Actually $(NUMERIC_VERSION) is more generic
omits c2e9391 Replace HTS_VERSION with hts_version()
omits 750f564 Use config.h for configuration options
omits fcb9563 constify input parameter to faidx_fetch_seq
omits 8256ea8 Use strtoul() for other unsigned 'B' types too
omits 83a9bdd Use strtoul instead of strtol for XX:B:I tags so that integers >2.14 billion work.
omits 4b8c9b5 Bug fix to stop sam view from converting 'H' into 'Z' types.
omits ab92989 Bug fix to handle blank headers in SAM files
omits 6d9e20e Update kstring.[ch] from upstream sources
omits 039620b Update khash.h from upstream sources
omits 13698ea Added tests/test_view
omits 956f45b bgzf.c: Check return status of bgzf_read_block in bgzf_useek to catch gzipped (as opposed to bgzipped) files.
omits 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.
omits eeb41a7 Bug fix to khashification of process_one_read.
omits 1e6f3cf Added some synthetic SAM test data and a test perl script to trial conversion between SAM, BAM and CRAM. A work in progress.
omits 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).
omits 0649ecb Bug fix to khash-ification of sam_hdr_add_lines
omits e25066b Better handling of unknown references.
omits 016efd5 Use strtoul instead of strtol for XX:B:I tags so that integers >2.14 billion work.
omits 5500ef0 Bug fix to stop sam view from converting 'H' into 'Z' types.
omits fa5d1a1 Bug fix to handle blank headers in SAM files.
omits 417fc59 Switch from modifying CFLAGS to CPPFLAGS so we can do "make CFLAGS=-g".
omits 47b7241 Further removal of various unusued portions of Staden io_lib.
omits 6df8103 Merge branch 'develop' of https://github.com/samtools/htslib into develop
omits e79e112 Major overhaul of CRAM code (originally imported from Samtools/htlib branch, and further back from Staden Package io_lib).
omits 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)
omits 6799348 Build shared libraries, add "make install" target
omits f455afd New non-recursive build infrastructure
omits dd9c5a2 Lift library source to the top-level directory
omits ad5ee37 Remaining application code also moving repository
omits 7413bed Deleted files which were moved to the new samtools/bcftools.git repository
omits 7508806 Merge branch 'develop' of github.com:samtools/htslib into develop
omits 3c4259c vcfcheck: re-enabled stats by QUAL
omits cbc4478 Test with both Clang and GCC
omits 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.
omits bdb550f Move format specifications to sam-spec repository
omits 779e243 Merge remote branch 'remotes/sm15-mod/develop' into develop
omits 3ecd0cb vcfsubset: Make --apply-filters consistent with other tools
omits dbcc082 Resolved vcfmerge.c merge conflict
omits e47feba vcf core lib, vcfsubset, vcfmerge: First step towards binary BCF output. Functional but probably buggy.
omits 348c5a1 Merge branch 'master' into develop
omits 0fb04c2 Add Travis CI control file
omits eedca8d Merge branch 'razf_sync' of https://github.com/mp15/htslib into develop
omits 0670753 Merge branch 'for-samtools' into develop
omits c3d530e vcffilter: Change in neighbourhood function in SOM training, seems more robust with respect to random seed
omits 8496905 Avoid conflicting with samtools's bam_index()
omits b267fb4 Expose bam_hdr_init() in the public API header
omits 7a5992c vcfnorm: Removed two assertions to allow realignment of MNPs
omits efa9530 vcfcheck: Fixed a bug in initialization of frame-shift calculation; More detailed FS output
omits 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.
omits 0c275f6 Maintain the same API regardless of -D BGZF_MT
omits 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 "."
omits e567ef0 Add klist.h, as used by samtools
omits 1994af5 vcfsubset: New -i,-e options for general filter expressions. In this version, only QUAL and INFO columns are supported.
omits 4523040 plot-vcfcheck: Produce the overlap by AF graphs
omits 45be6fe vcffilter,gtcheck: Added sanity checks; Extended help message; Changed the order of columns on gtcheck output
omits 72b5b28 vcfcheck: Changed output format of Ts/Tv
omits d30f1aa resolved test/check.chk conflict
omits 8876289 Replace with samtools's ksort
omits 3f76a40 Updated tests
omits 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.
omits 49f9e95 vcfmerge, vcfnorm: Append command and version string to VCF header
omits 5da7aef vcf.[hc]: API to update FILTER column. BCF output not supported yet in this version
omits db1edf3 vcfutils: bcf_gt_type should not be declared as static
omits c420b54 add tests for vcfsubset
omits a7f4597 add new tool vcfsubset
omits a7f24e2 deal with Number=A and Number=G INFO and FORMAT fields when trimming alleles
omits c9873a3 correct typos
omits e91d10b tbx: Allow indexing of empty files, do not segfault
omits b281180 vcfview: Fix in bcf_subset; force unpacking on VCF output
omits ac479c3 Merge changes from samtools's kstring
omits a458ed8 Fix <stdarg.h> include
omits c3622b8 Revert to kstring.h with a separate kstring.c
omits f15f7bc vcfcheck: More readable output, replace "-" by "<STDIN>" when reading from standard input
omits 8b095aa Port fixes from samtools razf.c/h to htslib.
omits 8e14b56 vcfcheck: create additional ts/tv stats which counts 1st alternate allele only
omits f344f7a vcffilter: skip the two additional score fields when applying SOM filters
omits 222fe6c vcffilter: First step towards indel filtering - new switch to select from good sites mask
omits fb0d88d vcfmerge: Fixed subtle bugs revealed when merging FMT fields of different lengths; Append version string and command to the output VCF header
omits 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.
omits 12b827f vcfcheck: Fixed a bug introduced by recent changed in synced reader
omits 429216a vcffilter: backup commit, bad SOM now working
omits f6c95a1 Merge remote branch 'mp15/develop' into develop
omits 5d717a2 vcfmerge, vcfisec: Change in synced reader's API, allow unlimited number of input files. (Previously the limit was sizeof(int)*8)
omits 99b8b89 Add const to char *'s to ensure they can be called with fixed values without triggering compiler warnings
omits ce6022e Import header comments from samtools
omits 46a4b6a Use sizeof() and NULL instead of numbers
omits 974d20b Fix crash on legacy files
omits 6a5a672 vcffilter: Plot also bad sites in annotation distributions. Updated test files.
omits f4bfe4a vcfquery: Enable -p option again
omits 1dbfae8 vcfisec: in the sites output mode print also file mask
omits 7d76f62 vcffilter: check to prevent division by zero in the python plot script
omits 89f7e5d gtcheck: fixed incorrect output, instead of uncertainty, the opposite (confidence) was reported before
omits 944c4b0 vcfmerge: fix of copy-and-paste error in format field merging, use correct integer ranges
omits 35ed1b5 vcfgtcheck: Fix in INFO/DP parsing, wrong ID was used before
omits 54868e8 vcffilter: Plot also cropped annotation distributions to show the range of values actually used in filtering
omits 1ed4f54 vcfmerge: do not crash with non-overlapping chromosomes
omits aae973b vcfview: Restored the subset functionality (continued)
omits eaee02d vcfview: Restored the subset functionality
omits b1c5fea vcffilter: plot annotation distributions
omits 19ca371 vcffilter: allow arbitrary order in -f and -l filtering options (X>value is same as value<X)
omits d01fcee vcffilter: extended help message
omits 84901c3 bcf1_update_info fix: initialize bcf_info_t pointer, do not pass NULL
omits 4cf9350 vcffilter: fixed a typo, output file names now named correcly based on filter type
omits 7141bd5 vcfcheck: Do not run in streaming mode with the -t option
omits d09058b vcfcheck: complain if tabix index not available with -t option
omits 2f5843a vcfquery fix: Allow a mask file with the -v option
omits 73f147b A few bugfixes from the previous two commits. New -S option in gtcheck and -H made work also in the cross-check mode
omits eef8320 gtcheck: Removed forgotten debugging line
omits 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 [...]
omits 5b0880e vcfcheck: Do not crash at non-variant sites. Restore checking of two VCFs.
omits 6d906ba core vcf: added API for modifying/deleting/adding INFO fields, currently only VCF output supported; vcfmerge: AN,AC tags now updated correctly.
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reference pointing at a previous point in the repository history.
* -- * -- N refs/heads/master (1c631e9)
\
O -- O -- O (9469458)
Any revisions marked "omits" are not gone; other references still
refer to them. Any revisions marked "discards" are gone forever.
No new revisions were added by this update.
Summary of changes:
.gitignore | 21 +-
.travis.yml | 8 -
Makefile | 295 +-
README.md | 10 +-
abreak.c | 197 +
bam2bed.c | 64 +
bam2fq.c | 116 +
bamidx.c | 20 +
bamshuf.c | 141 +
bcfidx.c | 17 +
config.h | 3 -
cram/cram.h | 66 -
cram/cram_codecs.c | 1761 ---
cram/cram_codecs.h | 155 -
cram/cram_decode.c | 2114 ----
cram/cram_decode.h | 112 -
cram/cram_encode.c | 2630 -----
cram/cram_encode.h | 105 -
cram/cram_index.c | 385 -
cram/cram_index.h | 98 -
cram/cram_io.c | 3606 -------
cram/cram_io.h | 523 -
cram/cram_samtools.c | 144 -
cram/cram_samtools.h | 97 -
cram/cram_stats.c | 357 -
cram/cram_stats.h | 59 -
cram/cram_structs.h | 750 --
cram/files.c | 76 -
cram/mFILE.c | 593 -
cram/mFILE.h | 87 -
cram/md5.c | 295 -
cram/md5.h | 54 -
cram/misc.h | 110 -
cram/open_trace_file.c | 386 -
cram/open_trace_file.h | 115 -
cram/os.h | 306 -
cram/pooled_alloc.c | 170 -
cram/pooled_alloc.h | 56 -
cram/sam_header.c | 1222 ---
cram/sam_header.h | 452 -
cram/string_alloc.c | 153 -
cram/string_alloc.h | 69 -
cram/thread_pool.c | 713 --
cram/thread_pool.h | 197 -
cram/vlen.c | 432 -
cram/vlen.h | 48 -
cram/zfio.c | 185 -
cram/zfio.h | 54 -
debian/changelog | 16 -
debian/compat | 1 -
debian/control | 55 -
debian/copyright | 143 -
debian/gbp.conf | 15 -
debian/htslib-test.install | 1 -
debian/libhts-dev.install | 5 -
debian/libhts0.install | 2 -
debian/libhts0.symbols | 509 -
debian/rules | 22 -
debian/source/format | 1 -
debian/source/options | 1 -
debian/watch | 3 -
doc/.gitignore | 32 +
doc/BCFv2.tex | 95 +
doc/index.tex | 64 +
faidx.5 | 124 -
hfile.c | 438 -
hfile.h | 194 -
hfile_internal.h | 58 -
hfile_net.c | 82 -
htslib.mk | 114 -
htslib/Makefile | 31 +
bgzf.c => htslib/bgzf.c | 495 +-
htslib/bgzf.h | 122 +-
faidx.c => htslib/faidx.c | 136 +-
htslib/faidx.h | 13 +-
hts.c => htslib/hts.c | 331 +-
htslib/hts.h | 107 +-
htslib/kfunc.h | 49 -
htslib/khash.h | 161 +-
htslib/klist.h | 121 -
knetfile.c => htslib/knetfile.c | 7 +-
htslib/kseq.h | 5 -
htslib/ksort.h | 157 +-
htslib/kstring.h | 170 +-
razf.c => htslib/razf.c | 25 +-
htslib/razf.h | 4 +-
sam.c => htslib/sam.c | 447 +-
htslib/sam.h | 86 +-
htslib/synced_bcf_reader.c | 809 ++
htslib/synced_bcf_reader.h | 190 +-
tbx.c => htslib/tbx.c | 27 +-
htslib/tbx.h | 7 +-
vcf.c => htslib/vcf.c | 1198 +--
htslib/vcf.h | 558 +-
htslib/vcf_sweep.h | 15 -
htslib/vcfutils.c | 257 +
htslib/vcfutils.h | 37 +-
htslib_vars.mk | 19 -
kfunc.c | 254 -
kstring.c | 229 -
main.c | 224 +
misc/plot-vcfcheck | 1579 +++
sam.5 | 45 -
samview.c | 70 +
synced_bcf_reader.c | 1190 ---
tabix.c | 82 +
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 | 150 -
test/ex1.gtf.gz | Bin 0 -> 3778 bytes
test/{test-vcf-api.out => ex2.vcf} | 15 +-
test/ex3.sam | 14 +
test/fieldarith.c | 48 -
test/fieldarith.sam | 15 -
test/hfile.c | 179 -
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/tabix.2.3199812.out | 1 +
test/test-vcf-api.c | 156 -
test/test-vcf-sweep.c | 87 -
test/test-vcf-sweep.out | 4 -
test/test.pl | 100 +-
test/test_view.c | 114 -
test/test_view.pl | 49 -
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 | 96 -
vcf_sweep.c | 158 -
vcfcheck.c | 802 ++
vcffilter.c | 1243 +++
vcfgtcheck.c | 587 +
vcfisec.c | 387 +
vcfmerge.c | 1097 ++
vcfnorm.c | 648 ++
vcfquery.c | 703 ++
vcfutils.c | 458 -
vcfview.c | 107 +
183 files changed, 10969 insertions(+), 48655 deletions(-)
delete mode 100644 .travis.yml
create mode 100644 abreak.c
create mode 100644 bam2bed.c
create mode 100644 bam2fq.c
create mode 100644 bamidx.c
create mode 100644 bamshuf.c
create mode 100644 bcfidx.c
delete mode 100644 config.h
delete mode 100644 cram/cram.h
delete mode 100644 cram/cram_codecs.c
delete mode 100644 cram/cram_codecs.h
delete mode 100644 cram/cram_decode.c
delete mode 100644 cram/cram_decode.h
delete mode 100644 cram/cram_encode.c
delete mode 100644 cram/cram_encode.h
delete mode 100644 cram/cram_index.c
delete mode 100644 cram/cram_index.h
delete mode 100644 cram/cram_io.c
delete mode 100644 cram/cram_io.h
delete mode 100644 cram/cram_samtools.c
delete mode 100644 cram/cram_samtools.h
delete mode 100644 cram/cram_stats.c
delete mode 100644 cram/cram_stats.h
delete mode 100644 cram/cram_structs.h
delete mode 100644 cram/files.c
delete mode 100644 cram/mFILE.c
delete mode 100644 cram/mFILE.h
delete mode 100644 cram/md5.c
delete mode 100644 cram/md5.h
delete mode 100644 cram/misc.h
delete mode 100644 cram/open_trace_file.c
delete mode 100644 cram/open_trace_file.h
delete mode 100644 cram/os.h
delete mode 100644 cram/pooled_alloc.c
delete mode 100644 cram/pooled_alloc.h
delete mode 100644 cram/sam_header.c
delete mode 100644 cram/sam_header.h
delete mode 100644 cram/string_alloc.c
delete mode 100644 cram/string_alloc.h
delete mode 100644 cram/thread_pool.c
delete mode 100644 cram/thread_pool.h
delete mode 100644 cram/vlen.c
delete mode 100644 cram/vlen.h
delete mode 100644 cram/zfio.c
delete mode 100644 cram/zfio.h
delete mode 100644 debian/changelog
delete mode 100644 debian/compat
delete mode 100644 debian/control
delete mode 100644 debian/copyright
delete mode 100644 debian/gbp.conf
delete mode 100644 debian/htslib-test.install
delete mode 100755 debian/libhts-dev.install
delete mode 100755 debian/libhts0.install
delete mode 100644 debian/libhts0.symbols
delete mode 100755 debian/rules
delete mode 100644 debian/source/format
delete mode 100644 debian/source/options
delete mode 100644 debian/watch
create mode 100644 doc/.gitignore
create mode 100644 doc/BCFv2.tex
create mode 100644 doc/index.tex
delete mode 100644 faidx.5
delete mode 100644 hfile.c
delete mode 100644 hfile.h
delete mode 100644 hfile_internal.h
delete mode 100644 hfile_net.c
delete mode 100644 htslib.mk
create mode 100644 htslib/Makefile
rename bgzf.c => htslib/bgzf.c (61%)
rename faidx.c => htslib/faidx.c (78%)
rename hts.c => htslib/hts.c (76%)
delete mode 100644 htslib/kfunc.h
delete mode 100644 htslib/klist.h
rename knetfile.c => htslib/knetfile.c (99%)
rename razf.c => htslib/razf.c (98%)
rename sam.c => htslib/sam.c (70%)
create mode 100644 htslib/synced_bcf_reader.c
rename tbx.c => htslib/tbx.c (86%)
rename vcf.c => htslib/vcf.c (53%)
delete mode 100644 htslib/vcf_sweep.h
create mode 100644 htslib/vcfutils.c
delete mode 100644 htslib_vars.mk
delete mode 100644 kfunc.c
delete mode 100644 kstring.c
create mode 100644 main.c
create mode 100755 misc/plot-vcfcheck
delete mode 100644 sam.5
create mode 100644 samview.c
delete mode 100644 synced_bcf_reader.c
create mode 100644 tabix.c
delete mode 100644 test/aux#aux.sam
delete mode 100644 test/aux.fa
delete mode 100644 test/aux.fa.fai
delete mode 100644 test/c1#bounds.sam
delete mode 100644 test/c1#clip.sam
delete mode 100644 test/c1#pad1.sam
delete mode 100644 test/c1#pad2.sam
delete mode 100644 test/c1#pad3.sam
delete mode 100644 test/c1.fa
delete mode 100644 test/c1.fa.fai
delete mode 100644 test/ce#1.sam
delete mode 100644 test/ce#2.sam
delete mode 100644 test/ce#5.sam
delete mode 100644 test/ce#5b.sam
delete mode 100644 test/ce#large_seq.sam
delete mode 100644 test/ce#tag_depadded.sam
delete mode 100644 test/ce#tag_padded.sam
delete mode 100644 test/ce#unmap.sam
delete mode 100644 test/ce#unmap1.sam
delete mode 100644 test/ce#unmap2.sam
delete mode 100644 test/ce.fa
delete mode 100644 test/ce.fa.fai
create mode 100644 test/check.chk
create mode 100644 test/check.vcf
delete mode 100755 test/compare_sam.pl
create mode 100644 test/ex1.gtf.gz
rename test/{test-vcf-api.out => ex2.vcf} (57%)
create mode 100644 test/ex3.sam
delete mode 100644 test/fieldarith.c
delete mode 100644 test/fieldarith.sam
delete mode 100644 test/hfile.c
create mode 100644 test/isec.a.vcf
create mode 100644 test/isec.ab.C.out
create mode 100644 test/isec.ab.any.out
create mode 100644 test/isec.ab.both.out
create mode 100644 test/isec.ab.out
create mode 100644 test/isec.b.vcf
create mode 100644 test/isec.tab
create mode 100644 test/isec.tab.out
create mode 100644 test/merge.a.chk
create mode 100644 test/merge.a.vcf
create mode 100644 test/merge.abc.out
create mode 100644 test/merge.b.vcf
create mode 100644 test/merge.c.vcf
create mode 100644 test/norm.fa
create mode 100644 test/norm.fa.fai
create mode 100644 test/norm.out
create mode 100644 test/norm.vcf
create mode 100644 test/query.out
create mode 100644 test/query.vcf
create mode 100644 test/tabix.2.3199812.out
delete mode 100644 test/test-vcf-api.c
delete mode 100644 test/test-vcf-sweep.c
delete mode 100644 test/test-vcf-sweep.out
delete mode 100644 test/test_view.c
delete mode 100755 test/test_view.pl
delete mode 100644 test/xx#blank.sam
delete mode 100644 test/xx#large_aux.sam
delete mode 100644 test/xx#large_aux2.sam
delete mode 100644 test/xx#minimal.sam
delete mode 100644 test/xx#pair.sam
delete mode 100644 test/xx#rg.sam
delete mode 100644 test/xx#triplet.sam
delete mode 100644 test/xx#unsorted.sam
delete mode 100644 test/xx.fa
delete mode 100644 test/xx.fa.fai
delete mode 100644 vcf.5
delete mode 100644 vcf_sweep.c
create mode 100644 vcfcheck.c
create mode 100644 vcffilter.c
create mode 100644 vcfgtcheck.c
create mode 100644 vcfisec.c
create mode 100644 vcfmerge.c
create mode 100644 vcfnorm.c
create mode 100644 vcfquery.c
delete mode 100644 vcfutils.c
create mode 100644 vcfview.c
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