[med-svn] [htslib] branch upstream updated (b9d85dc -> 0b1efff)
Andreas Tille
tille at debian.org
Mon Dec 11 13:58:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository htslib.
from b9d85dc Merge tag '1.3.2' into debian/unstable
adds cf5950e Added reference to tabix
adds 97b7373 New upstream version
adds e79fb0a Add remark about pristine-tar commit
adds 82819fe Upload to unstable
adds 6fb42cf Add build-essential to autopkgtest
adds e9945fc debhelper 10
adds f24104e d/watch: version=4
adds 1b39d8d Add @builddeps@ to autopkgtest
adds 536682b Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable
adds 78d31d7 Added ref to OMICtools
adds 44f77d5 Install header files from cram dir in -dev package since these are used in libseqlib
adds e4ea80c Fix pkg-config
adds 54feaaa Upload to experimental
adds d8c1ca3 Removed use of CRAM "CORE" block while encoding.
adds 543f030 Add {errmod,kprobaln,bam_md}.[ch] from samtools
adds 96acc6c Retain only library parts of realn.c; canonicalise whitespace
adds 55b2ae4 Add errmod declarations to htslib/hts.h and errmod.o to Makefile
adds 1e6909b Rename kpa_glocal() to probaln_glocal() and add to htslib/hts.h
adds 8439061 Rename as sam_cap_mapq()/sam_prob_realn() and add to htslib/sam.h
adds 622bfaa Remove probaln_par_def/probaln_par_alt constants
adds b183ab2 Add errmod / probaln / prob_realn to HTSlib API (PR #343)
adds 10e3c2c Remove unused variable [minor]
adds 0454d47 Fix len parameter type [minor]
adds 6d70a0e Create API to check EOF on all htsFile that support EOF block
adds f2399ee New bam_mplp_reset function to allow mplp in multiple regions
adds cd2d915 Fix potential infinite loop [minor]
adds 1385d7a Replace bcf_hdr_fmt_text(), which can't handle huge headers
adds cb92f20 Read BCF header's l_text as unsigned
adds f581de8 Merge fixes for huge BCF headers (PR #373)
adds 1cc7d12 Add curl_kput(), which slurps an URL into a kstring
adds fc062fb knetfile.c: Only emit Range header if needed
adds b64e076 Make hts_itr_query find no-coor reads when last reference is unused.
adds ab793a8 Don't assume order of sequence_ids when finding HTS_IDX_NOCOOR location.
adds 375ba53 Merge hts_itr_query(HTS_IDX_NOCOOR) fixes (PR #376)
adds e5ab997 Fixed out by one error in bin calculation (CRAM -> BAM).
adds 21e6a8f Reorder Makefile dependencies [minor]
adds abfd337 Use internal plain char isdigit_c()/etc ctype functions
adds 5720e3e Deleted the broken code in zfopen() when HAVE_POPEN is defined.
adds e1dd635 Sam_index_build(2) now returns -4 for failure to save/create the index.
adds 43a94fb Write CRAM ref cache via hFILE rather than stdio
adds bb03b02 Added bam_aux_update_str()
adds f58922d Add doxygen @file documentation
adds 4eef9a7 Fixed CRAM MD/NM generation to follow the same logic as calmd.
adds 67234cb Make kstring detect more errors and work better on 64 bit systems
adds 02220bf Use hts_get_bgzfp() when format.compression==bgzf
adds 481752c Not with tabs, James! [minor]
adds 11661a5 Show coordinates in "unsorted positions" error message
adds 4b1610f Added a lossy read-name option (CRAM_OPT_LOSSY_NAME).
adds 4c0b93b Made the CRAM_OPT_PREFIX option external via the "name_prefix" option.
adds f689e18 Merge CRAM lossy name compression (PR #326)
adds 53b5f5d Expose cram_get_refs() function to return the opaque refs_t data type.
adds d496268 allow bcf_index_build2 to index both bcf and vcf
adds b6aa0e6 Detect shared library and plugin types during configure
adds 3f41083 stringify_argv(): suppress trailing space
adds 1eec11b Fixes bug in bam_aux_update_str()
adds 2cddfb3 Build DLL and plugins on Cygwin
adds 3a8d3d3 Htslib now copes with zero length Z and H aux tags.
adds 4502742 Use hFILE rather than stdio when reading indices
adds 1c6cf22 Fixed file-descriptor leak in refs_load_fai().
adds 925a3c9 Document required Cygwin (and RPM-style) devel packages
adds 02e9d21 Add is_cram flag to distinguish dummy hts_itr_t objects
adds 155e1aa Add print-config target
adds 0de7fe5 Generate config.h.in with autoheader
adds 86260e1 Add configure check for fdatasync()
adds c6cb4c3 Use finer-grained $(INSTALL_LIB) and $(INSTALL_MAN) macros
adds 5869a67 hts_itr_query(): discard chunks far beyond the query region
adds 0d5a5eb Avoid linguist mis-classification [minor]
adds fd721f1 Allocate BGZF::uncompressed_block/compressed_block together
adds 344c825 Allow plugins to select RTLD_LOCAL or RTLD_GLOBAL
adds 0f2a88a Protect against sequences starting beyond reference end.
adds e8bddbe Use native Doxygen API documentation markup
adds e87ae87 Add interfaces to hfile for delimited string input
adds ed502be [faidx.h] Use native Doxygen API documentation markup
adds f86372e Remove iRODS plugin, which has moved to samtools/htslib-plugins
adds 74bcfd7 Embed version number directly in hfile_libcurl plugin
adds 23d7f17 Discard distant chunks based on binning index, not linear index
adds bbaab35 [tabix man page] Note coordinate arguments are 1-based inclusive
adds c31216b Added bgzf_block_write() and rebgzip option. Check indexing and rebgzip are not attempted simultaneously.
adds eaef296 Added bgzip test files. Add bgzip --rebzip test and update test files.
adds 54dc232 Rebased PR#387 and minor code formatting fixes (trailing white space, indentation, tabs) for consistency with existing code.
adds e79775f Added bgzip to check/test dependency.
adds 71db687 Treat regions [-1,n) as [0,n) when indexing
adds 8d957c0 Rewrite #ifdeffed-out use of now-removed variable [minor]
adds 503b09d Merge version number bump and NEWS file from master
adds bdf85e4 Speed up to probaln_glocal.
adds 88517df Added callback + client data hooks to pileup iterators and pileup struct.
adds 3566540 Factored in the renormalisation to the f[] computation.
adds 8c595df Cosmetic: 0 to NULL
adds f10f9b2 Bump SOVERSION to 2 and note ABI incompatibility in NEWS
adds bf75336 Merge (ABI-changing!) mpileup callbacks (PR #398)
adds 0ca17a0 Handle VCF lines with misssing `FORMAT=.`
adds 19c1894 Fix bugs in bam_aux_update_str()
adds 4295de4 Bug fix: 0 is a valid return value of bcf_hrec_find_key
adds 553406d Use <inttypes.h> instead of old WIN32-specific code
adds 519f75a Prompoted cram/thread_pool code to the top-level and use it within bgzf writing instead of its own multi-threading.
adds aaf998a Tidied up the mass of #ifdefs.
adds f72add4 Further updates to multi-threading.
adds 2cb33f9 Fixed dependencies & .mk defs so Samtools links too (threading change).
adds 70f1fae Fixed uninitialised memory (queue shutdown).
adds 242e03e Tidied up pointless while/if duplication. (Left over from a more complex structure.)
adds 6717817 Draft of the multi-threaded decoder.
adds 2ef8e3e Committing as it's a working MT decoder now.
adds 41a714a Attempt to use shared pool.
adds 121bab9 Major revamp of thread pool and associated tests. In particular the input queue is now per output queue rather than shared between all output queues. This helps resolve deadlocks and permits more advanced task sharing.
adds 5142d24 Bumped the sample size for the tests, and made all tests share a common size.
adds 8e9bd80 White space updates (tabs -> spaces).
adds 7d50ac6 Sorry, updates to the previous commits too; forgetting to add this file!
adds 0ba5636 Updates to cope with the new thread pool API.
adds 2af39f8 Removed some debugging and changed the default queue sizes to be smaller.
adds bd32ec6 Improvements to avoid boom & bust scenarios.
adds 8a8fac2 Culled the duplicate is_compressed assignment.
adds 2c2330b Various memory leaks fixed in bgzf multi-threading.
adds bedeccc First apparent working bgzf_seek implementation.
adds d6dacc7 Added HTS_OPT_CACHE_SIZE option to specify the bgzf cache size. This can speed up decoding considerably in certain circumstances.
adds f522f1f Made thread job serial numbers 64-bit.
adds 15ef81b Improvements to multi-threading encode/decode/transcode.
adds 1c0ff9d Changed the HTS_OPT_THREAD_POOL argument from a t_pool pointer to a t_pool plus queue size int. This is to permit one large queue for encoding side and lots of small queues on decoding side all sharing one pool; eg a many-way merge.
adds c721a74 bgzf_check_EOF now works when input is multi-threaded.
adds 9d2e3de Propagate read error in thread breader ack to fp->errcode error in main thread.
adds 511a235 Deleted the now defunct read_eof variable.
adds d0614e5 Fixed bgzf_getc and bgzf_getline to work in multi-threaded mode.
adds 8ca0175 Added support for multi-threaded BAM indexing.
adds e65f67d Fixed CRAM_OPT_THREAD_POOL for cram.
adds 173a5d0 Merge branch 'develop' of https://github.com/samtools/htslib into threading_pool
adds 93be96b Bug fix to hts_get_bgzfp.
adds d365af3 Improvements for VCF/BCF multi-threading.
adds ccd48bd Make sure we destroy the thread_pool when created by ourselves.
adds eceeb01 Merge branch 'develop' of https://github.com/samtools/htslib into threading_pool
adds 3ade6b6 Bug fix to bgzf_read, which was breaking samtools index (and more).
adds 4f29e22 PTHREAD_MUTEX_RECURSIVE_NP vs PTHREAD_MUTEX_RECURSIVE.
adds 7235947 Code tidyup.
adds 1659e8f test_view now also verified multi-threading.
adds cc4fe23 Removal of debugging output.
adds 3bfd281 Migrated the thread pool structures to thread_pool_internal.h.
adds c00fe2c Renamed various thread pool structs/functions.
adds 299c7b6 Culled the DEBUG_TIME code in thread_pool.
adds 5c59172 Further tidying up of queue vs process; mostly comments and docs.
adds 3d3cc32 Fixed a race condition in the multi-threaded cram encoder.
adds 5b31094 Fixed a double free in multi-threaded CRAM and regions.
adds b077a6b Replaced BSD license with MIT license for consistency.
adds 7a54ff9 Avoid extraneous #includes
adds daae2ea Merge threading pool API (PR #397)
adds d58eab8 Fix error handling in cram_index_load.
adds 6ff0ca0 Don't redefine thread_pool.h typedefs
adds 609120d More thorough INFO cleaning to prevent issues like https://github.com/samtools/bcftools/issues/428
adds f7370bb Activate auxf#values_java.cram test
adds 1bc5c56 Ensure headers compile by themselves [minor]
adds 50db54b Suppress index date warning when hts_verbose == 0
adds b2f29c8 Minor fix to lzma error message.
adds 3ea35c9 Added a safe_ltf8_decode function to go along with the itf8 variant.
adds c62d1ff Fixed multi threaded partial decoding. (Eg quitting after N reads)
adds f1eb18d Fixed a bug where we weren't setting fd->first_container on V2.x or V3.x files (io_lib r3789).
adds 22ef715 Code changes to synchronise cram_encode.c (mostly) with io_lib.
adds 6607907 Merged in several cram_codecs changes from io_lib.
adds 99f112c Improved error checking, copied over from io_lib.
adds a061cc2 Added a BASES_PER_SLICE hts option.
adds ee98182 CRAM encoding now puts auxiliary tags in their own blocks.
adds 370c1ed Add prototype for cram_update_curr_slice to avoid warning in cram_io.c.
adds 7bf85c2 Sped up rANS decoders by 6% (O0) to 10% (O1).
adds 293a426 Merge CRAM updates, sync with io_lib implementation (PR #361)
adds 7e6f35d Make cram_decode_estimate_sizes handle missing codecs.
adds be8b4a5 Ensures rANS uncompressors don't read beyond end of input.
adds 707f60a Merge pull request #438 from daviesrob/cram_afl
adds 7aa1ef8 Refactor incidental uses of kstream
adds 71c03b8 Remove htsFile's use of kstream
adds 6b9abba Add fixed/immobile hFILE buffers
adds 32984ca Implement base64-encoded data: URLs
adds 2520497 Add JSON format and very basic recognition
adds 274ef7d Add hopen() varargs; use them for HTTP headers in hfile_libcurl.c
adds 39ca089 Add JSON tokeniser / lexer
adds 941c043 Parse GA4GH Retrieval protocol and handle redirects
adds 5490930 Fix hseek() already-read buffer reuse bug
adds cc42613 Fix hFILE write-after-read bug
adds 82d0f5b Merge JSON-based GA4GH redirection file access protocol (PR #439)
adds ee47258 allele trimming bugfix
adds de69feb Also handle uncompressed (raw) BCF for vcf_sweep
adds c9e8f3a Prevents out-of-bounds array access on ref_id
adds 9ea1bf9 Adds more CRAM decoder checks to prevent overrunning input buffers
adds 1dd5c15 Fixes test for enough data when reading the preservation map.
adds 36c5c47 Prevents wrap-around bugs in allocations.
adds 677d9b0 Make hts_expand handle realloc failure a bit better.
adds 6ce295d Propagate error return codes from hts_getline()
adds 5dff82a Use hFILE to read htsFile::fn_aux FAI file
adds 47a29fd Make htsfile work with (e.g. GA4GH) redirects
adds 4ef6c76 Fixed a rare renormalisation bug in the rANS codec.
adds 7def9fd Constify extern tbx_conf_* preset variables
adds 468abb6 Turn off autodetection when -s,-b,-e,-0,-c,-S, or -p are given
adds 8efbd1b Add missing entries
adds afd9b56 Define _XOPEN_SOURCE so that PTHREAD_MUTEX_RECURSIVE is defined
adds 37c85e4 Prevent reads past the end of the VCF header.
adds cc6ca52 Make bcf_read1_core() return error if ks_resize fails, or on short read.
adds d3ac0db Add function bcf_record_check() to validate bcf records
adds 6d927df Change bam1_core_t::n_cigar from uint16_t to uint32_t
adds 092b5aa Happy New Year
adds 5d114eb Alter bam1_t data layout so that CIGAR data is 32-bit aligned
adds 59972b7 Fix test/compare_sam.pl -Baux on 32-bit platforms
adds c8475e8 Support custom S3 endpoint host_base setting (in .s3cfg)
adds 1901451 vcfutils: replace exit() with return -1 in bcf_remove_allele_set
adds 515fd20 propagate vcf errors from synced reader
adds 2c75e79 Add "httphdr", "httphdr:l", and "va_list" hopen() options
adds 63fe9d1 Add support for Google Cloud Storage pseudo-URLs
adds f3a3a80 Merge Google Cloud Storage support (PR #446)
adds acbd58e Permit CRAM lossy_names mode to accept TLEN 0 or TLEN +/- 1.
adds 28aa45f Ensure max_off is -1 when end bin overflows
adds 3046bbf Extended bcf_get_format*() documentation to emphasize difference between ndst and the return value. Correspondingly extended the bcf_get_gentotypes() example. See pull request #308.
adds 038a61b Fix whitespace, shorten help string [minor]
adds 1bd62b3 Split S3 parts of hfile_libcurl.c into separate hfile_s3.c
adds 70f2cc8 Move S3 support from hfile_libcurl.c to hfile_s3.c
adds 481ba66 Merge separate hfile_s3.c code
adds e7bf06f Don't FAILONERROR at high verbosity and other minor libcurl changes
adds 2448fd5 Add `htsfile -cv` raw view mode for unknown file formats
adds ec1d68e Add bgzf_compression(); reuse check_header() in bgzf_is_bgzf()
adds 0e63e29 Fixed dead-lock case in seek + multi-threaded decode.
adds 271cbaa Added a kputd for %g specialisation.
adds da61ad5 kputd: set kstring len correctly for negative exponential values
adds 2916d7c Merge PR #395 (Add a kputd for %g specialisation).
adds 255863e Adjusted prototype for kputd to be consistent with other kput functions.
adds f476b53 Fixed bgzf threading dead-lock when trying to reading beyond EOF.
adds 2e0e124 BGZF skip empty blocks, do not give up reading prematurely
adds 99660e0 Report missing BGZF EOF blocks
adds d8d0323 Fixes for dealing with raw gzip streams.
adds 942f5d2 Stop test_cmd from merging stderr with its output.
adds 86e32e9 Add hts_endian.h to convert little-endian bytes to/from native integers.
adds 70622cf Fix undefined behaviour and improve endian-related behaviour
adds 12d6e02 Merge commit PR #459 (Fix undefined behaviour and improve endian-related behaviour)
adds 79f38a3 Include <sys/select.h>
adds 0452e7e Further thread pool fixes.
adds 190a722 Merge "Further thread pool fixes" branch (PR #465)
adds fd178d3 Fixed bgzf_gzip_compress when given uncompressable data.
adds ff71a31 Fixed data corruption when switching to threads part way through a stream.
adds 3dc96c5 Allow fai index to be in a different location to the indexed file.
adds 2e1c10b Add bgzf_index_load_hfile and bgzf_index_dump_hfile
adds 84a89da Add bgzf unit tests
adds 9e2fbac Remove MacOS X dead-lock in bgzf threading.
adds ee2bcaa Add more error checks when building indexes
adds 7bfa010 Add tabix functional tests
adds 95b1034 Remove abort on corrupt aux data, pass errors up instead
adds 8dd26ff Make sam_format1() fail it it finds an invalid aux type
adds dc54b0d Fix to iterators when the query overlaps zero bins.
adds 7317e4f Fix endianness, integer type and memory safety issues in index metadata
adds 0c32631 bcf_index_build3: return -4 on index write failure as per sam_index_build3
adds 1c3c77a Mention thread pool changes.
adds 6e89752 Provide more informative error message when unknown SAM tag type is encountered.
adds be9736d Undefine macro after it has served its purpose (no functional change).
adds 1b5652c Merge "Provide more informative error message for unknown tag type (PR#444)"
adds 4021753 Add BZ2/LZMA to configure.ac and infrastructure to config.pc.in
adds a6842b5 Fixed lzma memory limit.
adds c010cc3 Document the --disable-lzma and --disable-bz2 configure options
adds 2434a5a Add -rdynamic/-ldl to htslib.pc.in's static_* variables when needed
adds 57c7105 Deal with bzip2 pkg-config module not being available everywhere
adds e37732b Add more libraries to static_LIBS, where required
adds 9558a72 Create a Makefile fragment with static linking flags
adds 06edd7e Remove explicit -lz -lm link flags; add to LIBS instead
adds a2d7f07 Merged PR#463 (Configure BZ2/LZMA and make htslib.pc more accurate).
adds 811d30f News updates (from historical commits).
adds ae0bec6 Prevent segfault due to VCFs with very large IDX tag values
adds 442ae75 Fixed a few non-portable constructs.
adds 30b9f50 Added a description of how the thread pool test program works.
adds c6d1c34 Added missing #include in test_view.c.
adds 6a44f49 Reworked synced VCF/BCF reading
adds efbded0 Default to check for libcurl; don't fail on no -lcrypto for s3 check
adds b1a193c Add libbz2 and liblzma to default libraries in the Makefile
adds 03452dd Add sections on dependencies and making configure to the INSTALL file.
adds 078069b Travis updates.
adds 5c695a1 Prevent infinite loop on empty indexes
adds ca1423d Fix over-specified location of htslib.pc.tmp
adds d2d9c76 Release 1.4: summary
adds 0172fe3 Merge tag '1.4' into debian/unstable
adds 94d9711 New upstream version
adds e742362 Update patches
adds 46d5eee Drop autoconf from Build-Depends, add libbz2-dev and liblzma-dev to Build-Depends
adds 28af9f8 Remove binary files from test results
adds f711b01 Remove symbols file since I'm too lazy to maintain these - volunteers welcome for a final upload to instable
adds d6ae67d hange library name to match soname
adds 02e2be3 Include htsfile binary into tabix package since its used by manta package
adds 903f2b3 Upload to experimental
adds d6cab91 add the cram_to_bam function to the public interface of htslib because it is used by code in Sambamba
adds e880f57 Use -lpthread instead of -pthread when only linking; Fixes clang warning
adds 879855b Merge version number bump and NEWS file from master
adds e2a1f18 Merge PR #255 into develop.
adds e2a5578 Added tabix to the "make test" dependency.
adds 10bc1a7 Tweak to tabix long opts to remove duplicate 'h'.
adds 10081c4 add test-bcf-sr to .gitignore [minor]
adds 9986f5d Fixed kputd printing of NaN.
adds 3a31ddf Add check for libsocket to autoconf (needed to compile on illumos/Solaris)
adds 052a16e Merge check for libsocket (commit 3a31ddf from PR#488)
adds e7203ae Fixed a bug in bcf_fmt_array with garbage allele frequencies. The special value 0x7f800001 (NaN), used to indicate a missing value, was changed to 0x7fc00001 (also NaN) when the function le_to_float returned.
adds 150334c Handling of float-type missing values in VCF files, part 2 of 3: bcf_get_info_values.
adds dd0c31d Handling of float-type missing values in VCF files, part 3 of 3: bcf_get_format_values.
adds cf469f6 Replaced memcpy with the more descriptive bcf_float_set_missing in vcf_parse.
adds 55e6404 oops
adds b7bb8c7 Reordered test cases so that the output file ends up the way it's supposed to.
adds 9db2e71 Made the changes slightly smaller through the use of bcf_float_set.
adds 487f367 Merge Merge NaN issue fix (PR#485)
adds a17fc73 Fixes to support a stricter C99 plus POSIX.1-2001 environment.
adds 65267c7 Replaces the itf8* macro abominations with static inline functions.
adds b30fc6a Tidy up non-standard C99 issues.
adds ff8f83a Merge C99 compliance improvements (PR#498)
adds af89ccb Free file name strings upon successful faidx loading
adds 9317ca6 Ensure B aux tags have a comma after the type charater
adds 1acad45 Fix buffer overrun on corrupted data.
adds 1e1bf97 Harden rANS decoding against malicious or random input.
adds b1b2816 CRAM check for embedded references being too small for slice.
adds 2270547 Further rANS protections.
adds 0f60c35 Ensure BGZF block length is longer than the block header
adds 42bfe70 Check number of symbols is sensible in Huffman codec stream
adds 6a50863 Make bcf_set_variant_type() aware of breakends
adds bb15901 Improve end of name detection in fai_read
adds cd26782 Improve fai_fetch() and faidx_fetch_seq()
adds 74cd222 Prevent fai_retrieve() from reading one character too many
adds 8e1be4a Change isspace to isspace_c
adds ae4f3df Ensure bcf_hdr_read() is reading vcf or bcf
adds 079c7b8 Limit query name to 251 bytes to prevent l_qname overflow
adds 8e96d8a Bug fix in VCF/BCF header parsing
adds affe5c0 Ensure bcf_hdr_t is destroyed when bcf_hdr_parse() fails
adds 94accfc Ensure bcf_hdr_parse_line() always finishes at the next newline or NUL
adds b8c6f7d Simplify bcf_hdr_parse()
adds 72a7c2a Trivial SAM header sanitising.
adds 0639ea1 Improve sam_hdr_sanitise()
adds 89ea70a NEWS update. (#529)
adds 6c06833 Release 1.4.1: summary
adds e8b1b66 Merge tag '1.4.1' into debian/unstable
adds 68e8b57 New upstream version
adds 04bb939 Upload to unstable
adds ab6cc2a Create symlinks only for arch=indep target when target dir exists
adds b8c5413 Upload to unstable
adds 485cda1 fix FTBFS
adds 942393b Fix FTBFS on s390x and sparc64
adds 7b16102 Dereference symlinks to fix autopkgtest
adds 7771288 Merge version number bump and NEWS file from master
adds 6163114 First draft of a new logging mechanism.
adds e1848ae Added helper macros log_error, log_error, etc.
adds ddcc3ab Switched to new logging functions in bgzf.c. NOTE suspicious buggy bracket placements on lines 1716 and 1752 (before edit) changed.
adds c54f23c Added tests for logging.
adds c6d03a1 Adapted to gcc/unix environment.
adds 08c16ef Moved the declaration of hts_log & co to the public API. Appended the hts_ prefix to the log_<level> macros. Switched to standard C99 __VA_ARGS__ instead of ##__VA_ARGS__. Added HTS_FORMAT checking to the hts_log function. Changed the initialization of hts_verbose to use the literal HTS_LOG_INFO instead of magic number 3. Centralized newline handling to the hts_log function. Re-purposed the test-logging.pl script to test for message consistency.
adds 0d3d32f Restored the default log level (3) but now interpreted as HTS_LOG_WARNING. Added HTS_LOG_TRACE log level.
adds ea59199 Adjusted log levels in bgzf.c.
adds 49fe80f Added trace log level to get_severity_tag.
adds 0cad436 Add htslib/hts_log.h to htslib_vars.mk and htslib.mk
adds 0664276 Adjusted log levels for a few messages
adds e66ab04 Make hts_log() preserve errno.
adds 3e85cce Merge logging mechanism (PR #499)
adds a58cd85 Bug fix to CRAM index creation (reported by Brent Pedersen).
adds 499245e Added a PTHREAD_MUTEX_RECURSIVE check.
adds a7df765 Fix buffer overrun in vcf_format.
adds 4051805 Also added Number= checking for INFO headers.
adds 15b2f21 Remove read-past-buffer when printing error message.
adds c4deecd Additional argument protection in sam_hdr_write and bcf_hdr_write.
adds 31650a4 Prevent out of bounds read on BAM_CIGAR_STR by extending to 16 bytes
adds d8e5ec4 Fix clang warning
adds 54bfd95 Fix length calculation in bam_read1 and possible memory leak
adds f613867 Limit subexp and gamma decoders to integer cram_external_type
adds df51916 Additional error checking for invalid CRAM ref_id.
adds 389c4f3 Replaced fprintf(stderr, ...) calls with hts_log_<level> calls. Fixed a few cases of irregular indentation in the process. Made the logging test script ignore multi-line messages.
adds 1189660 Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
adds dc45f18 Cosmetic improvements to the error messages.
adds 403353f Fixed format string errors.
adds fe2627f Merge Logging improvements 2 (PR #543) into develop
adds a0fe63f Use BGZF* in cram_index_build() instead of zfp*
adds 5b9361d Removed the (>20 year old!) unnecessary vlen.[ch] code.
adds 979571b Allow out to be NULL in cram_huffman_decode_char()
adds 7fd21f5 Adds HTS_OPT_BLOCK_SIZE support for SAM/BAM/CRAM.
adds 8d201be Added dependency from knetfile.c to hts_log.h, with some cascading. Added missing dependencies to the Makefile, including the missing definition of htslib_hts_h.
adds f0fc3ee Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
adds 03c4be2 Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
adds 3c0302d Use htslib_hts_log_h definition from htslib_vars.mk
adds f1b95e1 Merge branch 'pr551' into pr551_merge
adds b28aa8d Remove autom4te.cache during `make distclean`
adds 3872861 Updated NEWS file for Solstice release.
adds fba943d Stop threaded bgzf_read_block from using stale values at EOF
adds 49fdfbd Relase 1.5: Solstice
adds ffd8e11 Merge tag '1.5' into debian/unstable
adds ada885d New upstream version
adds 8ce1126 Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable
adds d3b4f02 Standards-Version: 4.0.0 (no changes needed)
adds e335d9b do not parse d/changelog explicitly
adds bee0b75 Refresh patches
adds 3ccc8bd hardening=+all
adds 7654192 install htslib*.mk files that are used in bcftools
adds cd80951 libhts-dev: Depend on missing liblzma-dev
adds ff8e09b Wrap and sort
adds f45af8d Finalize changelog for 1.5-1
adds 08915d9 Fix OMICS entry
adds 49237db Apply patch provided by Graham Inggs <ginggs at debian.org> to fix FTBFS on armel armhf and ppc64el of bcftools
adds ca1cd8b Standards-Version: 4.1.1
adds 0071935 Revert "Remove symbols"
adds 517d1b8 update symbols file names to current SOVERSION name
adds 0a86645 Remove missing symbols
adds eaa8b36 Update symbols file for 1.4.1
adds e6cfeed Remove ks_destroy, ks_getuntil2, ks_init
adds 7b50daf Update symbols file for 1.5
adds b481c8a Update symbols files for 1.5 cram symbols
adds e73fa42 Update changelog with work on symbols file
adds 2823ef8 Import Debian changes 1.5-2
adds 6940ebf Merge tag 'debian/1.5-2' into debian/unstable
adds 5540e88 Update 877670.patch as it was applied upstream
adds 6474772 Indicate closes Bug 879886
adds 7d3f63e release to unstable
adds 020aa90 Fix build on i386
adds fe81062 Upload to unstable
adds 1bfbb49 Extend i386 fix to hurd and kfreebsd
adds 092b0c9 Fix FTCBFS: Let dh_auto_configure pass --host to ./configure
adds 5e812e2 Procide cram headers in separate package libhts-private-dev.install
adds 6863c08 Deactivate fix_pkg-config.patch
adds 6fd2321 Close according bug
adds 4ff741a Add versioned breaks
adds 030a92f Standards-Version: 4.1.2
adds 64f8109 Test is using private headers
adds 3a01f34 Upload to unstable
adds 5fedaea Do not install htslib*.mk fragments
adds 30646ba Upload to unstable after verifying that bcftools does not need these htslib*.mk fragments
new a7cd55f New upstream version 1.5
new 0b1efff New upstream version 1.6
The 2 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:
.appveyor.yml | 43 +
.gitattributes | 12 -
.gitignore | 37 -
.travis.yml | 8 -
INSTALL | 110 +-
Makefile | 316 ++++--
NEWS | 159 +++
README.md | 33 -
bcf_sr_sort.c | 661 ++++++++++++
bcf_sr_sort.h | 103 ++
bgzf.c | 1335 ++++++++++++++++-------
bgzip.c | 57 +-
config.h.in | 38 -
config.mk.in | 56 +-
configure.ac | 268 ++++-
cram/cram_codecs.c | 269 +++--
cram/cram_codecs.h | 4 +
cram/cram_decode.c | 256 +++--
cram/cram_encode.c | 960 +++++++++--------
cram/cram_encode.h | 10 +
cram/cram_external.c | 19 +-
cram/cram_index.c | 177 +--
cram/cram_index.h | 4 +-
cram/cram_io.c | 730 ++++++-------
cram/cram_io.h | 294 ++++-
cram/cram_samtools.c | 17 +-
cram/cram_samtools.h | 2 +-
cram/cram_stats.c | 274 +----
cram/cram_structs.h | 60 +-
cram/mFILE.c | 43 +-
cram/mFILE.h | 5 +
cram/open_trace_file.c | 1 -
cram/os.h | 120 +--
cram/pooled_alloc.h | 2 +
cram/rANS_byte.h | 18 +-
cram/rANS_static.c | 241 +++--
cram/sam_header.c | 11 +-
cram/string_alloc.c | 2 +-
cram/thread_pool.c | 757 -------------
cram/thread_pool.h | 218 ----
cram/vlen.c | 430 --------
cram/vlen.h | 48 -
cram/zfio.c | 183 ----
cram/zfio.h | 62 --
debian/README.source | 34 -
debian/changelog | 112 --
debian/compat | 1 -
debian/control | 85 --
debian/copyright | 117 --
debian/gbp.conf | 15 -
debian/htslib-test.install | 7 -
debian/libhts-dev.install | 6 -
debian/libhts1.install | 2 -
debian/libhts1.lintian-overrides | 2 -
debian/libhts1.symbols | 639 -----------
debian/patches/define_PATH_MAX.patch | 37 -
debian/patches/literal_version.patch | 16 -
debian/patches/series | 2 -
debian/rules | 38 -
debian/source/format | 1 -
debian/source/options | 2 -
debian/tabix.install | 2 -
debian/tabix.links | 1 -
debian/tabix.lintian-overrides | 3 -
debian/tabix.manpages | 1 -
debian/tests/control | 3 -
debian/tests/run-unit-test | 19 -
debian/upstream/tabix.edam | 16 -
debian/watch | 3 -
errmod.c | 196 ++++
faidx.c | 455 ++++----
hfile.c | 310 ++++--
hfile_gcs.c | 137 +++
hfile_internal.h | 51 +-
hfile_irods.c | 259 -----
hfile_libcurl.c | 842 +++++++--------
hfile_s3.c | 467 ++++++++
hts.c | 783 ++++++++++----
hts_internal.h | 96 ++
htslib/vcf_sweep.h => hts_os.c | 43 +-
htsfile.1 | 9 +-
htsfile.c | 191 ++--
htslib.mk | 31 +-
htslib.pc.in | 15 +-
htslib/bgzf.h | 110 +-
htslib/cram.h | 37 +-
htslib/faidx.h | 188 ++--
htslib/hfile.h | 194 ++--
htslib/hts.h | 203 +++-
htslib/hts_defs.h | 26 +-
htslib/hts_endian.h | 354 ++++++
htslib/hts_log.h | 93 ++
htslib/{vcf_sweep.h => hts_os.h} | 48 +-
htslib/knetfile.h | 3 +-
htslib/ksort.h | 11 +-
htslib/kstring.h | 99 +-
htslib/regidx.h | 12 +-
htslib/sam.h | 188 +++-
htslib/synced_bcf_reader.h | 59 +-
htslib/tbx.h | 9 +-
htslib/thread_pool.h | 290 +++++
htslib/vcf.h | 120 ++-
htslib/vcf_sweep.h | 5 +-
htslib/vcfutils.h | 18 +-
htslib_vars.mk | 9 +-
knetfile.c | 33 +-
kstring.c | 126 ++-
md5.c | 3 +-
multipart.c | 264 +++++
plugin.c | 10 +-
probaln.c | 285 +++++
realn.c | 199 ++++
regidx.c | 56 +-
sam.c | 792 ++++++++++----
synced_bcf_reader.c | 291 ++---
tabix.1 | 14 +-
tabix.c | 54 +-
tbx.c | 89 +-
test/aux#aux_java.cram | Bin 3774 -> 0 bytes
test/auxf#values.sam | 4 +-
test/auxf#values_java.cram | Bin 0 -> 5152 bytes
test/bgziptest.txt | 1 +
test/bgziptest.txt.gz | Bin 0 -> 181 bytes
test/bgziptest.txt.gz.gzi | Bin 0 -> 88 bytes
test/compare_sam.pl | 24 +-
test/cross_validate.sh | 4 +-
test/{formatcols.vcf => formatmissing-out.vcf} | 2 +-
test/{formatcols.vcf => formatmissing.vcf} | 2 +-
test/hfile.c | 48 +-
test/hts_endian.c | 510 +++++++++
test/md#1.sam | 12 +
test/md.fa | 3 +
test/md.fa.fai | 1 +
test/sam.c | 209 +++-
test/tabix/bed_file.Y.100200.out | 1 +
test/tabix/bed_file.bed | 39 +
test/tabix/gff_file.X.2934832.2935190.out | 4 +
test/tabix/gff_file.gff | 70 ++
test/tabix/large_chr.20.1.2147483647.out | 9 +
test/tabix/large_chr.vcf | 18 +
test/tabix/tabix.tst | 65 ++
test/tabix/test-tabix.sh | 183 ++++
test/tabix/vcf_file.1.3000151.out | 1 +
test/tabix/vcf_file.2.3199812.out | 1 +
test/tabix/vcf_file.vcf | 36 +
test/test-bcf-sr.c | 141 +++
test/test-bcf-sr.pl | 548 ++++++++++
test/test-bcf-translate.c | 192 ++++
test/test-bcf-translate.out | 18 +
test/test-logging.pl | 96 ++
test/test-regidx.c | 18 +-
test/test-vcf-api.c | 119 +-
test/test.pl | 149 ++-
test/test_bgzf.c | 782 ++++++++++++++
test/test_view.c | 74 +-
htslib/vcf_sweep.h => test/thrash_threads1.c | 56 +-
htslib/vcf_sweep.h => test/thrash_threads2.c | 54 +-
htslib/vcf_sweep.h => test/thrash_threads3.c | 59 +-
test/thrash_threads4.c | 68 ++
test/thrash_threads5.c | 66 ++
test/thrash_threads6.c | 108 ++
test/thread_pool.md | 58 +
textutils.c | 379 +++++++
thread_pool.c | 1373 ++++++++++++++++++++++++
thread_pool_internal.h | 165 +++
vcf.c | 960 ++++++++++++-----
vcf_sweep.c | 4 +-
vcfutils.c | 246 ++++-
version.sh | 31 +
win/rand.c | 98 ++
win/rand.h | 24 +
171 files changed, 17045 insertions(+), 7882 deletions(-)
create mode 100644 .appveyor.yml
delete mode 100644 .gitattributes
delete mode 100644 .gitignore
delete mode 100644 .travis.yml
delete mode 100644 README.md
create mode 100644 bcf_sr_sort.c
create mode 100644 bcf_sr_sort.h
delete mode 100644 config.h.in
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/README.source
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/libhts1.install
delete mode 100644 debian/libhts1.lintian-overrides
delete mode 100644 debian/libhts1.symbols
delete mode 100644 debian/patches/define_PATH_MAX.patch
delete mode 100644 debian/patches/literal_version.patch
delete mode 100644 debian/patches/series
delete mode 100755 debian/rules
delete mode 100644 debian/source/format
delete mode 100644 debian/source/options
delete mode 100644 debian/tabix.install
delete mode 100644 debian/tabix.links
delete mode 100644 debian/tabix.lintian-overrides
delete mode 100644 debian/tabix.manpages
delete mode 100644 debian/tests/control
delete mode 100644 debian/tests/run-unit-test
delete mode 100644 debian/upstream/tabix.edam
delete mode 100644 debian/watch
create mode 100644 errmod.c
create mode 100644 hfile_gcs.c
delete mode 100644 hfile_irods.c
create mode 100644 hfile_s3.c
copy htslib/vcf_sweep.h => hts_os.c (61%)
create mode 100644 htslib/hts_endian.h
create mode 100644 htslib/hts_log.h
copy htslib/{vcf_sweep.h => hts_os.h} (53%)
create mode 100644 htslib/thread_pool.h
create mode 100644 multipart.c
create mode 100644 probaln.c
create mode 100644 realn.c
delete mode 100644 test/aux#aux_java.cram
create mode 100644 test/auxf#values_java.cram
create mode 100644 test/bgziptest.txt
create mode 100644 test/bgziptest.txt.gz
create mode 100644 test/bgziptest.txt.gz.gzi
copy test/{formatcols.vcf => formatmissing-out.vcf} (83%)
copy test/{formatcols.vcf => formatmissing.vcf} (83%)
create mode 100644 test/hts_endian.c
create mode 100644 test/md#1.sam
create mode 100644 test/md.fa
create mode 100644 test/md.fa.fai
create mode 100644 test/tabix/bed_file.Y.100200.out
create mode 100644 test/tabix/bed_file.bed
create mode 100644 test/tabix/gff_file.X.2934832.2935190.out
create mode 100644 test/tabix/gff_file.gff
create mode 100644 test/tabix/large_chr.20.1.2147483647.out
create mode 100644 test/tabix/large_chr.vcf
create mode 100644 test/tabix/tabix.tst
create mode 100755 test/tabix/test-tabix.sh
create mode 100644 test/tabix/vcf_file.1.3000151.out
create mode 100644 test/tabix/vcf_file.2.3199812.out
create mode 100644 test/tabix/vcf_file.vcf
create mode 100644 test/test-bcf-sr.c
create mode 100755 test/test-bcf-sr.pl
create mode 100644 test/test-bcf-translate.c
create mode 100644 test/test-bcf-translate.out
create mode 100755 test/test-logging.pl
create mode 100644 test/test_bgzf.c
copy htslib/vcf_sweep.h => test/thrash_threads1.c (59%)
copy htslib/vcf_sweep.h => test/thrash_threads2.c (62%)
copy htslib/vcf_sweep.h => test/thrash_threads3.c (58%)
create mode 100644 test/thrash_threads4.c
create mode 100644 test/thrash_threads5.c
create mode 100644 test/thrash_threads6.c
create mode 100644 test/thread_pool.md
create mode 100644 textutils.c
create mode 100644 thread_pool.c
create mode 100644 thread_pool_internal.h
create mode 100755 version.sh
create mode 100644 win/rand.c
create mode 100644 win/rand.h
--
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