[med-svn] [htslib] branch debian/unstable updated (53af783 -> 98c18ca)
Charles Plessy
plessy at moszumanska.debian.org
Sat Aug 16 09:40:28 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository htslib.
from 53af783 Updated symbols again.
adds f192318 vcf: Support for IDX BCF tag
adds 0c084f2 vcf: Output . for missing INFO, FMT and samples
adds 9029156 vcf.c: Fixed a renaming artifact, bcf_clear1 should be bcf_clear
adds 9d6defa vcf: qual now set to missing on bcf_clear; Avoid warnings about type-punned pointers
adds 997c519 Output VCFv4.2 header
adds ebd9b94 Cope with empty containers internal to a CRAM stream. Technically empty containers shouldn't exist as the specification states they must contain at least one block. However this is a useful precursor to the EOF block checking.
adds 3e96dd7 Added implementation of cram_external_encode(). It's not yet used except in experimental versions, but opens up the route to storing more CORE data in external blocks to make partial decoding simpler (eg CRAM->FASTA).
adds 70efcd9 Bug fix to the zlib strategy tuning in multi-threaded mode. It could (legitimately) drive the number of trials negative, but this meant it never left the trial phase and consequentially encoding speed more or less halved the instant we asked for more than one encoding thread.
adds a935e3c Added refs_t->last_id (note distinct from ->last) for use when reading from MD5 server. This reduces excessive reloading of the file in certain cases.
adds 1a39edb Add mfsteal to mFILE, and use it in cram_populate_ref.
adds 34227f8 Added missing return code checks. Fixed 'x' mode of mfreopen.
adds b5ccf9b Merge branch 'develop' into bcftools+calling
adds 06208f2 Updated test
adds ea4dbc6 add support for Number=R fields when trimming alleles
adds cfdc6fd vcf: Make sure fileformat is added only once
adds 78a6ef3 Merge branch 'develop' of git://github.com/samtools/htslib into feature/number_R
adds 312add9 vcf: New bcf_get_info_string() wrapper
adds f78d671 vcf: New API bcf_get_format_string()
adds 2b801d7 add support for Number=R fields when trimming alleles
adds 0caf597 Allow overriding default columns indexes in bcf_sr_regions_init
adds c7c3ada vcf: new function bcf_remove_filter()
adds 36a8ce9 Merge branch 'develop' into bcftools+calling
adds 03f3fd7 Merge branch 'bcftools+calling' into develop
adds 4855f43 vcf: fix in bcf_get_genotypes, sanity check too strict for GT
adds b57379f vcf: Tip to workaround missing contig tags
adds b2aab8b hts indexing: Allow arbitrary chromosomal order.
adds 2d0423a vcf: New bcf_hdr_id2hrec() and bcf_hrec_format() functions
adds 96132f4 vcf: New vcf_write_line() function
adds 600acc3 synced_bcf_reader: New bcf_sr_seek() function
adds e7ffc82 vcf: New bcf_translate() and bcf_hdr_combine() API
adds 60c22d4 idx: Support for "." queries to retrieve all records
adds 4622eaf vcf: New bcf_has_filter() API function
adds 9dbf592 Fix hseek() return value test
adds 2daf614 Make filename argument a *const* char pointer
adds 650202c Strict matching of strings in bam_str2flag
adds b729954 vcf: new experimental bcf_hdr_set_samples() for subsetting
adds 0eb4c88 Merge branch 'bcftools+calling' into develop
adds 68848e2 bcf_hdr_set_samples() recognise lists vs file names
adds fd657c4 Store readrec function pointer within hts_itr_t
adds a60ff3f Make search key arguments *const* char pointers
adds a8be0b8 Write strcmp() comparisons comprehensibly
adds f0fb825 Add basic test exercising bcf_itr_queryi and bcf_itr_querys
adds 4d123f2 hts_itr_querys() calls hts_itr_query() via a function parameter
adds 655edab Add sam_itr_*() dealing with BAM and CRAM iterators interchangeably
adds 42152a6 synced_reader: Better handling of target alleles
adds ad17bb8 bcf_sr_set_samples to use the new --sample convention
adds fde4bd9 vcf: New bcf_get_info_flag() API
adds a6cbed2 Added some EOF block creation and checking.
adds ae92627 Bug fix to cram_next_slice(). The new while loop checking for non-empty blocks caused a crash when multi-threading.
adds 3a4aac5 Bug fix to EOF block writing when in multi-threaded mode (not yet supported in htslib's cram interface). It was writing the EOF block before flushing any pending threads.
adds dc4d0f1 Added a check to EOF in Cram in hts_close(). Note that this isn't the same place that BAM checks as it does it in hts_open(), however the benefit of doing on close is that this check can work when inputting from a pipe.
adds edb12c3 Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds 76cfc12 Updated the Cram EOF block detection to avoid falsely considering the lack of an EOF block as an error when doing a sub-range query.
adds 939f6ea Merge branch 'develop' of https://github.com/samtools/htslib into develop
adds 19ccc09 Fixed initialisation of CRAM indexing when the CRAM file contains refids that aren't sequential.
adds c68d523 Initialise beg and end values in the hts iterator. Without these mpileup simply bails out after fetching the first column as end is 0.
adds 843a063 Fixed the iterator to be 1-based inclusive coordinates for CRAM.
adds 025ecb3 Also initialise tid in case user code looks at it
adds 0e76a59 Merge pull request #46, CRAM EOF blocks
adds bae6c41 vcf: Abort on broken VCFs with multiple/trailing spaces/tabs
adds 0038f9e vcf: Don't let unpack_*_core forget the to-be-freed pointer
adds c62982e hts_expand0: type ptr properly, it can be of different type
adds b932f95 The default CRAM version is now 2.1. This is now the official release for supporting EOF blocks and the Java implementation only enforces them for CRAM 2.1 and above.
adds 322b28b Fixed EOF check. The usual code path had the correct check, but an empty cram triggered the incorrect code.
adds dc45cfc Bug fix to the SAM header padding. It could go negative and then fail to write the header.
adds 2279b3e Merge pull request #60, CRAM EOF block improvements
adds 85b864f To avoid confusion, make bcf_get_*_int and bcf_update_*_int symetric
adds aac5df5 hts_idx_load: Print warning when index is older than data
adds 5e03160 Make synced reader aware of bcf_hdr_set_sample(), expanded docs
adds 2eb509e Reduced the number of realloc calls zlib_mem_inflate(), while hopefully not overallocating much either.
adds 728ad50 Merge pull request #62, minor CRAM updates
adds d4d37c0 synced_reader: New bcf_sr_region_done macro
adds 5a340a1 Check cram_eof() before calling cram_close()
adds 39558ce bcf_translate: Catch unchecked errors
adds c336894 More sensible Quals of matching bases in overlaps
adds bcbfe37 Ignore operation-not-supported errors in fd_flush
adds c38cf60 Keep the style of the surrounding code
adds bdb6a4a Add HTS_IDX_NONE and document HTS_IDX_*
adds f6c37a5 Fixes incorrect MD5 calculation in cram_write_SAM_hdr
adds 21ca653 Merge #68, fix incorrect length given to MD5 calculation
adds 3ea22a1 Add 'a' (append) mode letter; propagate mode letters
adds 0d95c21 Add "data:blahblah" in-memory hFILE backend (read-only)
adds cb7f6e9 fix remote fetching of regions for bam and vcf
adds babaaf3 Use hFILE rather than knet in test_and_fetch()
adds 1069b17 Merge #70, fetching of remote BAM/VCF indices
adds 78e237b Fixed a bug when loading in fasta files consisting of all sequence on a single line and in lowercase.
adds 5c65920 vcf: Allow omitted trailing FORMAT fields
adds 692bb41 Fix sam_format1 failure on lines ending in integer/float tags and issue #63
adds 30b4033 Rewrite __skip_tag() as skip_aux()
adds ab84296 Add sam aux field tests
adds 20df6b9 Merge sam_format1() and __skip_tag() fixes (PR #73)
adds 5bdc06d synced_reader: Init position correctly
adds c6f8531 Add ks_release() to kstring.h
adds 321c402 Reinstate bam_header_dup as bam_hdr_dup
adds fb23174 Fix typo in comment
adds fee84e0 synced_reader: Init position correctly
adds fca50b8 Merge branch 'develop' into bcftools+calling
adds 1435a5d Merge branch 'develop' into bcftools+calling
adds d91c9bb Merge branch 'bcftools+calling' into develop
adds fe173b6 Make hfile.h part of the public API
adds d7f0ae1 Add MIT/Expat license boilerplate
adds 0180921 Define __attribute__ macros in a new (semi-public) header
adds ec3a15a Fixed comment typo
adds 22dedbe Merge pull request #79 from spalte/comment_typo
adds cc207d8 hts_idx: fixed indexing of NO_COOR blocks
adds cf693ad This resolves #49
adds d66571e Propagate error codes for CRAM_OPT_RANGE
adds 3490604 vcf: Propagate error in bcf_hdr_append
adds 9d640ff Fixed off-by-one in bcf_get_format_values
adds 9dec00e Construct HTS_IDX_REST and HTS_IDX_NONE iterators without an index
adds b26a445 Propagate error from bcf_hdr_printf
adds f7953db hts_readlist modifed to explicitly indicate file name vs list
adds acfeb8a make sure we have found values for AC _and_ AN before using
adds 5c80322 Merge pull request #82 from sm15/feature/bcf_calc_ac_bugfix
adds 503c95a Support for =X cigars in mpileup overlaps.
adds bb4721c faidx: Set error status if unknown seq is queried
adds cd410e1 Add duplication function for the bam1_t interface
adds 42d6aa1 Merge bam_dup1() addition (PR #80)
adds 3e52ddb Migrate documentation from samtools bam.h to sam.h and add a few more items
adds 128d97d bcf_hdr_subset: To allow sanity checks, mark missing samples
adds 52ecc97 bcf_sr_seek to seek to start with seq=NULL
adds eed28cb bcf_remove_alleles: Fix indexing range for Number=A alleles
adds df2c538 Silence -Wstrict-prototypes warnings
adds 388abc7 Fixed BCF output after bcf1_sync_alleles, simplified
adds 4a5dcf4 bcf_remove_alleles to work with BCF output
adds f5c96ca Added bgzip and tabix
adds bd6ed8b .gitignore tabix and bgzip
adds 20b6f6d Create trunk copy
adds 8b14e7f Change copyright notices now that MIT has approved open source distribution.
adds 4c42d43 Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
adds 0d51797 initial source code. It is BUGGY!
adds 7d22a01 bgzip is more like gzip in its command-line interface
adds dcd2f78 * tabix-0.0.0-1 (r500) * apparently working
adds e0afbb5 * tabix-0.0.0-2 (r501) * accelerate ti_readline()
adds 0f56c58 * tabix-0.0.0-3 (r502) * support meta lines (not tested) * I am going to make the index file in the BGZF format
adds 05df526 * tabix-0.0.0-4 (r503) * index files are bgzf compressed
adds e7dc13d * tabix-0.0.0-5 (r504) * fixed a critical bug in fetching data (a typo in fact) * support SAM (tested on ex1.sam) and VCF (not tested) * improve the command-line interface
adds 446b6e4 documentation
adds f667bfc Release tabix-0.1.0
adds a2d85ec Release tabix-0.1.1
adds 81170d8 * tabix-0.1.3 (r543) * fixed another off-by-one bug
adds f79c886 removed a line of debugging code
adds 15159c7 Added the -l option for listing chromosomes
adds ac9fc9f Fix in src/dst file detection and slight change of behaviour
adds 7cacea8 The behaviour changed slightly to mimic gzip. Detect if std descriptors are connected to the terminal.
adds 79d6239 * added the format specification * fixed a typo in bgzip
adds 4fb1b67 * tabix-0.1.3-2 (r555) * do not overwrite index file by default * a little code cleanup
adds 9b14f2c * tabix-0.1.3-3 (r556) * fixed a small memory leak in knetfile * fixed a minor bug for remote downloading
adds 9f16a45 Release tabix-0.1.4 (r559)
adds 50f5b5c * Release tabix-0.1.5 (r560) * Improve seeking efficiency. Index file needs to be rebuilt.
adds cf389c2 If nothing bad happens, this will become 0.1.6
adds c6770bb Release tabix-0.1.6
adds 6fa709d * improved C/Perl APIs * added test for Perl * added an tiny example
adds bccdc09 Release tabix-0.2.0
adds a79e73a Release tabix-0.2.1
adds a39b546 Release tabix-0.2.2
adds 31c8bd3 Complain about not-bgzipped files and check for noncontinuous chromosome blocks
adds 07f01ed Fix: Exit with an error rather than segfault when index is not present and region is queried
adds 3c60871 fixed a bug in C/Java when n_off == 0
adds 128523b patches by Peter Chines
adds 2c0b7ee Added -h option to print header lines
adds 4a6e786 Disable "unknown target name or minus interval" warning.
adds bbcc0b2 Release tabix-0.2.3
adds 08d08a2 Prevent the common user mistake and check the timestamps of the vcf and index file
adds 4dedb83 Fix: Complain only when VCF is newer, not newer or same mtime
adds 1cdcb39 New -r (reheader) option for efficient header replacement.
adds 7d48a19 BED support
adds 70e9ba8 update to the latest bgzf.*
adds 87f69fe fixed two bugs due to recent changes
adds e4477ce update version number
adds 046c761 Release tabix-0.2.4 (r949)
adds bec709b Release tabix-0.2.5 (r964)
adds 8ff4c17 Querying remote files required -f option on some systems
adds 83afb06 updated BGZF
adds 46b2463 Added option for printing header lines only
adds c2a5899 Guess the filetype from the file extension when -p not given
adds 8abdff6 Assume GFF format when the file type cannot be guessed, as in the previous version
adds a33c73e Even better, do this only for reading
adds 1344d39 Fix: allow custom formats
adds f14716c More informative error message about missing or out-of-date tabix index
adds 8af2d0a Fix: do not drop first record with both -B and -h
adds a09bef9 -C to output lines not overlapping BED
adds c49a4ec bgzip now compiles
adds cf03c20 Use htslib's bgzf.h, faidx.h, and razf.h
adds 90ae62f Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
adds 716070d tview and bgzip: Check that the files are bgzipped, not gzipped.
adds 5c1e1bb bgzip: Do not overwrite input files when -b or -s are given
adds 0f9a088 Check return status of IO calls to prevent gcc 4.6.3 warnings
adds ec581d6 Merge tabix and samtools bgzip.c and tabix.c
adds 1d963d7 Initial version of bgzip and tabix with htslib.
adds f38b5e2 Merge bgzip.c and tabix.c/.1 history from github.com/samtools/tabix
adds e45b3f3 Fix bgzip and tabix dependencies and link commands
adds 35f4642 Exit statuses are non-negative
adds 5adb883 bcf_subset: Reset n_fmt fields when all samples are dropped
adds 6e2ebc4 synced_reader: Regions operate on two as well as three columns again
adds db8055a bcf1_sync: Update rlen for new records as well
adds 41e8793 Merge branch 'bcftools+calling' into develop
adds 104adb5 Silence -Wstrict-prototypes warning
adds 996b3c0 Check sam_open() and sam_close() return values
adds 1ce5791 bcf_write: sanity check the number of samples, resolves #55
adds 9ed346d Return "" from bam_flag2str(0) rather than NULL
adds e321182 Bug fix to CRAM indexing and index usage.
adds d3bf5b6 Fixed two small memory leaks.
adds 09ba271 Revert one of the previous memory leaks as it breaks multi-threading. I need to find a more suitable way to solve this. The memory leak is back, but it's tiny; essentially leaking the last (empty) container.
adds eb71ced Better fix for container memory leak.
adds 0557506 Merge CRAM indexing bug fixes (PR #85)
adds 5003f7b Add hts_set_threads() file I/O threading API
adds 70be28c Fix bgzf_write() and bgzf_flush_try() error handling
adds f99d5ba Fix bam_write1() error handling
adds a1fb3bd vcf_parse: Detect missing INFO values in vectors
adds f1f2950 Merge branch 'develop' into bcftools+calling
adds 9db893a For bcftools to work with CSI indexes up to 2^31-1
adds fc4a18b New bcf_hdr_[sg]et_version API; bcf_hdr_subset preserves VCF version
adds 8deb11d Merge branch 'bcftools+calling' into develop
adds dc9a0fe bgzf: Support for reading gzip-compressed files.
adds dd58092 Minor comment change
adds 02721b7 bgzf: Support for FCOMMENT gzip header
adds 165850e bgzf: Support the remaining optional GZIP header fields
adds 2cc7ea4 bcf_sr: New missed_reg_handler and bcf_sr_regions_flush() function
adds d49dfa6 vcf: New bcf_dup() function
adds 191be31 Changed the initial CRAM EOF value to be 1 (expected EOF) and then explicitly set it to 0 at the start of each slice decode.
adds e76b489 idx: Don't create broken .tbi or .csi when file unsorted (VCF/BCF/BAM)
adds 8d283ed Sanitised the setting of fd->empty_container into one place. This also fixes the samtools bug #146.
adds 7d11028 Fix forgotten s/razip/bgzip/
adds b3a7868 Remove RAZF source code
adds e7bd15c Check CIGAR string has fewer than 2^16 operators
adds 7e059de Add a comment to deobfuscate bam_cigar_type
adds b62e668 Fix "unrecognized CIGAR operator" diagnostic
adds be61038 Removed bogus "Unable to find ref name"* errors when converting a SAM file UR:local/path/name syntax and without finding an MD5 reference to use. The code previously went on to work fine as a subsequent refs2id call worked.
adds 6622a18 Add functions for idxstats
adds 885bba0 Improve hts_idx_get_stat to work for more file types
adds 416f02a Return 0/-1 rather than bool; parenthesise C macro
adds d3ec3e2 Merge API functions for index statistics (PR #83)
adds 34082df sam_hdr_write() now calls cram_load_reference if hts_set_fai_filename() has been called. Also refs_load_fai() now copes with being given foo.fa or foo.fa.fai and does the right thing.
adds 0c360be Check index file magic numbers and I/O
adds e8806c7 Fix endianness problems outwith CRAM code
adds 49610fc Set NM/MD creation to be on by default.
adds 97c1e18 synced_reader: Removed unused code
adds aa68a05 vcf: Change of bcf_hdr_add_sample() usage.
adds 252d27d Add sam_open_mode() API function
adds 7d61caf Remove val_unused -- use HTS_UNUSED instead
adds 53c3ba8 bcf_write: Error message instead of assert + propagate the error up
adds 6a5b9fd vcf_parse: Detect incorrect number of columns
adds 6172a08 vcf: Fix BCF syncing when only partially unpacked
adds 3cdd62f vcf: Fixes in bcf_translate
adds 0d4e155 bgzf: Do not end prematurely on non-critical Z_BUF_ERROR zlib error
adds c8c5b31 vcf: Fix bcf_hdr_id2hrec, col_type parameter is needed as well
adds aff3226 bcf_trim_als: Propagate error instead of assert
adds 9074f89 bcf_update_alleles: Reference length with INFO/END
adds a969d0f Fix in index initialization
adds 2504243 Fixed bug in bcf1_sync. The main cause of the bug is as follows: bcf_unpack(bcf_rec, BCF_UN_STR); bcf_update_id(bcf_rec, id); This causes bcf_rec->d.shared_dirty to be set. duplicate = bcf_dup(bcf_rec); This calls bcf1_sync(). Since bcf_rec->d.shared_dirty is set, the shared data is re-created in tmp.s, bcf_rec->shared.s is freed and bcf_rec->shared.s = tmp.s. However, bcf_rec->unpack_ptr and bcf_rec->d.info[i].vptr still point to the old shared.s region which is inv [...]
adds 3b87c0e Improved bug fix of bcf1_sync() from the commit 2504243:
adds 049f877 synced_reader: Consider non-variant sites as matching in comparisons
adds c158790 Add extern "C" around API to enable C++ linking
adds 5f406e5 Merge pull request #108 from MauricioCarneiro/develop
adds eb27d19 vcf: Detect broken structured header lines
adds 7d31af0 synced_reader: Logical complements of target regions
adds 663b9cf bgzf: Translate windows line endings
adds 56d740e bcf_hdr_combine: Check for tags of conflicting lengths
adds 642783e faidx: Exit with an error if run on gzip-ed files
adds cc23df1 Fixed REF_PATH to handle URLs better.
adds 42775eb Suppress compression suffix search on default EBI MD5 service
adds b7c2a46 Merge REF_PATH fixes and libcurl removal (PR #111)
adds fcd0bd8 vcf: Support for mpileup's symbolic <X> allele
adds 894ebcf On open failure, set errno instead of printing message
adds 5498c0a Expose bcf_hdr_parse
adds ac4f30f vcf: Expose bcf_hdr_sync() and hrec_add_idx()
adds e12c343 vcf: bcf_hdr_get_hrec() interface made more general
adds b039db8 mpileup: Support for cigar operator "P"
adds 51d9560 faidx: new faidx_has_seq() call
adds 17d3d47 faidx: Fixed copy-and-paste documentation error
adds 399b580 hts_file_type: correct return of FT_VCF_GZ
adds dedd405 Merge pull request #113 from mcshane/feature/hts_file_type_fix
adds 232b77b Don't call freeaddrinfo() when getaddrinfo() fails
adds 4b024e1 Bug fix in bcf_trim_alleles()
adds c95dbc5 mpileup: Support for cigar operation N
adds dde9bdb Rationalise include guard macro names
adds 949d267 Ensure installation directories are world-executable
adds 19b5a8e Omit control files and README.md from release tarballs
adds 7dcaf17 Add license file
adds 45aaa8b Add MIT/Expat license boilerplate
adds 8b17b24 Fix copy/pasto
adds aaf99a9 Files under cram/ are BSD-licensed
adds deecae2 Add copyright notices and licensing boilerplate
adds 8bb77cc Add klib copyright notices and licensing boilerplate
adds cf35bd6 Add copyright notices and licensing boilerplate
adds b61c691 Add copyright notices and licensing boilerplate
adds 5cb1182 Update copyright notices to reflect historic changes
adds 0b6597c Add copyright notices and licensing boilerplate
adds 9155cca Update copyright years to reflect historic changes
adds d9122b7 Add copyright notices and licensing boilerplate
adds b5fbf05 Add copyright notices and licensing boilerplate
adds 7d3c063 Add copyright notices and licensing boilerplate
adds f19ff09 Add copyright notices and licensing boilerplate
adds 61ad3a6 Add copyright notices and licensing boilerplate
adds 9fc07d5 Merge copyright notice and licensing boilerplate additions
adds e770a1b Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
adds 9e95d31 Link shared library against libm and libpthread
adds 64bebbb Create a pkg-config description for easy linking
adds c99ed6a bgzf_seek: Assign corect block_address (on behalf of Chris Smowton)
adds 0b0736a Add basic INSTALL and README files
adds f2af2ad Release 1.0: first released HTSlib package
new cc559b8 Merge branch 'master' into debian/unstable
new 08a1e4a New upstream release; no new license notice.
new 74b9d7b Build on the master branch.
new 98c18ca Updated symbols file.
The 4 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 | 4 +
INSTALL | 25 +
LICENSE | 69 ++
Makefile | 97 +-
README | 5 +
README.md | 25 +-
bgzf.c | 1080 +++++++++---------
bgzip.c | 284 +++++
cram/cram_codecs.c | 5 +-
cram/cram_decode.c | 62 +-
cram/cram_index.c | 160 ++-
cram/cram_index.h | 2 +-
cram/cram_io.c | 134 ++-
cram/cram_io.h | 15 +-
cram/cram_structs.h | 4 +-
cram/mFILE.c | 71 +-
cram/mFILE.h | 1 +
cram/open_trace_file.c | 131 +--
cram/sam_header.c | 4 +-
cram/sam_header.h | 8 +-
debian/changelog | 4 +-
debian/copyright | 14 +-
debian/gbp.conf | 2 +-
debian/libhts0.symbols | 1042 +++++++++---------
faidx.5 | 23 +
faidx.c | 548 +++++-----
hfile.c | 98 +-
hfile_internal.h | 23 +-
hfile_net.c | 25 +-
hts.c | 1943 ++++++++++++++++++---------------
htslib.mk | 44 +-
htslib.pc.in | 10 +
htslib/bgzf.h | 411 +++----
htslib/faidx.h | 124 ++-
hfile.h => htslib/hfile.h | 34 +-
htslib/hts.h | 218 ++--
htslib/hts_defs.h | 47 +
htslib/kfunc.h | 30 +-
htslib/khash_str2int.h | 36 +-
htslib/klist.h | 4 +-
htslib/knetfile.h | 26 +
htslib/kstdint.h | 64 --
htslib/kstring.h | 19 +-
htslib/razf.h | 134 ---
htslib/sam.h | 337 ++++--
htslib/synced_bcf_reader.h | 152 ++-
htslib/tbx.h | 67 +-
htslib/vcf.h | 619 +++++++----
htslib/vcf_sweep.h | 28 +-
htslib/vcfutils.h | 60 +-
htslib_vars.mk | 23 +-
kfunc.c | 26 +
knetfile.c | 17 +-
kstring.c | 25 +
razf.c | 856 ---------------
sam.5 | 23 +
sam.c | 2327 +++++++++++++++++++++------------------
synced_bcf_reader.c | 539 ++++-----
tabix.1 | 155 +++
tabix.c | 399 +++++++
tbx.c | 418 +++----
test/compare_sam.pl | 100 +-
test/fieldarith.c | 60 +-
test/hfile.c | 45 +-
test/sam.c | 143 +++
test/test-vcf-api.c | 113 +-
test/test-vcf-api.out | 12 +-
test/test-vcf-sweep.c | 41 +-
test/test.pl | 44 +-
test/test_view.c | 239 ++--
test/test_view.pl | 32 +-
vcf.5 | 24 +
vcf.c | 2595 +++++++++++++++++++++++++++++---------------
vcf_sweep.c | 24 +
vcfutils.c | 736 ++++++++-----
76 files changed, 10391 insertions(+), 7001 deletions(-)
create mode 100644 .gitattributes
create mode 100644 INSTALL
create mode 100644 LICENSE
create mode 100644 README
create mode 100644 bgzip.c
create mode 100644 htslib.pc.in
rename hfile.h => htslib/hfile.h (82%)
create mode 100644 htslib/hts_defs.h
delete mode 100644 htslib/kstdint.h
delete mode 100644 htslib/razf.h
delete mode 100644 razf.c
create mode 100644 tabix.1
create mode 100644 tabix.c
create mode 100644 test/sam.c
--
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