[med-svn] [htslib] branch debian/unstable updated (54feaaa -> 46d5eee)

Andreas Tille tille at debian.org
Tue Mar 21 18:04:32 UTC 2017


This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch debian/unstable
in repository htslib.

      from  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
       new  b2f29c8   Minor fix to lzma error message.
       new  3ea35c9   Added a safe_ltf8_decode function to go along with the itf8 variant.
       new  c62d1ff   Fixed multi threaded partial decoding. (Eg quitting after N reads)
       new  f1eb18d   Fixed a bug where we weren't setting fd->first_container on V2.x or V3.x files (io_lib r3789).
       new  22ef715   Code changes to synchronise cram_encode.c (mostly) with io_lib.
       new  6607907   Merged in several cram_codecs changes from io_lib.
       new  99f112c   Improved error checking, copied over from io_lib.
       new  a061cc2   Added a BASES_PER_SLICE hts option.
       new  ee98182   CRAM encoding now puts auxiliary tags in their own blocks.
       new  370c1ed   Add prototype for cram_update_curr_slice to avoid warning in cram_io.c.
       new  7bf85c2   Sped up rANS decoders by 6% (O0) to 10% (O1).
       new  293a426   Merge CRAM updates, sync with io_lib implementation (PR #361)
       new  7e6f35d   Make cram_decode_estimate_sizes handle missing codecs.
       new  be8b4a5   Ensures rANS uncompressors don't read beyond end of input.
       new  707f60a   Merge pull request #438 from daviesrob/cram_afl
       new  7aa1ef8   Refactor incidental uses of kstream
       new  71c03b8   Remove htsFile's use of kstream
       new  6b9abba   Add fixed/immobile hFILE buffers
       new  32984ca   Implement base64-encoded data: URLs
       new  2520497   Add JSON format and very basic recognition
       new  274ef7d   Add hopen() varargs; use them for HTTP headers in hfile_libcurl.c
       new  39ca089   Add JSON tokeniser / lexer
       new  941c043   Parse GA4GH Retrieval protocol and handle redirects
       new  5490930   Fix hseek() already-read buffer reuse bug
       new  cc42613   Fix hFILE write-after-read bug
       new  82d0f5b   Merge JSON-based GA4GH redirection file access protocol (PR #439)
       new  ee47258   allele trimming bugfix
       new  de69feb   Also handle uncompressed (raw) BCF for vcf_sweep
       new  c9e8f3a   Prevents out-of-bounds array access on ref_id
       new  9ea1bf9   Adds more CRAM decoder checks to prevent overrunning input buffers
       new  1dd5c15   Fixes test for enough data when reading the preservation map.
       new  36c5c47   Prevents wrap-around bugs in allocations.
       new  677d9b0   Make hts_expand handle realloc failure a bit better.
       new  6ce295d   Propagate error return codes from hts_getline()
       new  5dff82a   Use hFILE to read htsFile::fn_aux FAI file
       new  47a29fd   Make htsfile work with (e.g. GA4GH) redirects
       new  4ef6c76   Fixed a rare renormalisation bug in the rANS codec.
       new  7def9fd   Constify extern tbx_conf_* preset variables
       new  468abb6   Turn off autodetection when -s,-b,-e,-0,-c,-S, or -p are given
       new  8efbd1b   Add missing entries
       new  afd9b56   Define _XOPEN_SOURCE so that PTHREAD_MUTEX_RECURSIVE is defined
       new  37c85e4   Prevent reads past the end of the VCF header.
       new  cc6ca52   Make bcf_read1_core() return error if ks_resize fails, or on short read.
       new  d3ac0db   Add function bcf_record_check() to validate bcf records
       new  6d927df   Change bam1_core_t::n_cigar from uint16_t to uint32_t
       new  092b5aa   Happy New Year
       new  5d114eb   Alter bam1_t data layout so that CIGAR data is 32-bit aligned
       new  59972b7   Fix test/compare_sam.pl -Baux on 32-bit platforms
       new  c8475e8   Support custom S3 endpoint host_base setting (in .s3cfg)
       new  1901451   vcfutils: replace exit() with return -1 in bcf_remove_allele_set
       new  515fd20   propagate vcf errors from synced reader
       new  2c75e79   Add "httphdr", "httphdr:l", and "va_list" hopen() options
       new  63fe9d1   Add support for Google Cloud Storage pseudo-URLs
       new  f3a3a80   Merge Google Cloud Storage support (PR #446)
       new  acbd58e   Permit CRAM lossy_names mode to accept TLEN 0 or TLEN +/- 1.
       new  28aa45f   Ensure max_off is -1 when end bin overflows
       new  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.
       new  038a61b   Fix whitespace, shorten help string [minor]
       new  1bd62b3   Split S3 parts of hfile_libcurl.c into separate hfile_s3.c
       new  70f2cc8   Move S3 support from hfile_libcurl.c to hfile_s3.c
       new  481ba66   Merge separate hfile_s3.c code
       new  e7bf06f   Don't FAILONERROR at high verbosity and other minor libcurl changes
       new  2448fd5   Add `htsfile -cv` raw view mode for unknown file formats
       new  ec1d68e   Add bgzf_compression(); reuse check_header() in bgzf_is_bgzf()
       new  0e63e29   Fixed dead-lock case in seek + multi-threaded decode.
       new  271cbaa   Added a kputd for %g specialisation.
       new  da61ad5   kputd: set kstring len correctly for negative exponential values
       new  2916d7c   Merge PR #395 (Add a kputd for %g specialisation).
       new  255863e   Adjusted prototype for kputd to be consistent with other kput functions.
       new  f476b53   Fixed bgzf threading dead-lock when trying to reading beyond EOF.
       new  2e0e124   BGZF skip empty blocks, do not give up reading prematurely
       new  99660e0   Report missing BGZF EOF blocks
       new  d8d0323   Fixes for dealing with raw gzip streams.
       new  942f5d2   Stop test_cmd from merging stderr with its output.
       new  86e32e9   Add hts_endian.h to convert little-endian bytes to/from native integers.
       new  70622cf   Fix undefined behaviour and improve endian-related behaviour
       new  12d6e02   Merge commit PR #459 (Fix undefined behaviour and improve endian-related behaviour)
       new  79f38a3   Include <sys/select.h>
       new  0452e7e   Further thread pool fixes.
       new  190a722   Merge "Further thread pool fixes" branch (PR #465)
       new  fd178d3   Fixed bgzf_gzip_compress when given uncompressable data.
       new  ff71a31   Fixed data corruption when switching to threads part way through a stream.
       new  3dc96c5   Allow fai index to be in a different location to the indexed file.
       new  2e1c10b   Add bgzf_index_load_hfile and bgzf_index_dump_hfile
       new  84a89da   Add bgzf unit tests
       new  9e2fbac   Remove MacOS X dead-lock in bgzf threading.
       new  ee2bcaa   Add more error checks when building indexes
       new  7bfa010   Add tabix functional tests
       new  95b1034   Remove abort on corrupt aux data, pass errors up instead
       new  8dd26ff   Make sam_format1() fail it it finds an invalid aux type
       new  dc54b0d   Fix to iterators when the query overlaps zero bins.
       new  7317e4f   Fix endianness, integer type and memory safety issues in index metadata
       new  0c32631   bcf_index_build3: return -4 on index write failure as per sam_index_build3
       new  1c3c77a   Mention thread pool changes.
       new  6e89752   Provide more informative error message when unknown SAM tag type is encountered.
       new  be9736d   Undefine macro after it has served its purpose (no functional change).
       new  1b5652c   Merge "Provide more informative error message for unknown tag type (PR#444)"
       new  4021753   Add BZ2/LZMA to configure.ac and infrastructure to config.pc.in
       new  a6842b5   Fixed lzma memory limit.
       new  c010cc3   Document the --disable-lzma and --disable-bz2 configure options
       new  2434a5a   Add -rdynamic/-ldl to htslib.pc.in's static_* variables when needed
       new  57c7105   Deal with bzip2 pkg-config module not being available everywhere
       new  e37732b   Add more libraries to static_LIBS, where required
       new  9558a72   Create a Makefile fragment with static linking flags
       new  06edd7e   Remove explicit -lz -lm link flags; add to LIBS instead
       new  a2d7f07   Merged PR#463 (Configure BZ2/LZMA and make htslib.pc more accurate).
       new  811d30f   News updates (from historical commits).
       new  ae0bec6   Prevent segfault due to VCFs with very large IDX tag values
       new  442ae75   Fixed a few non-portable constructs.
       new  30b9f50   Added a description of how the thread pool test program works.
       new  c6d1c34   Added missing #include in test_view.c.
       new  6a44f49   Reworked synced VCF/BCF reading
       new  efbded0   Default to check for libcurl; don't fail on no -lcrypto for s3 check
       new  b1a193c   Add libbz2 and liblzma to default libraries in the Makefile
       new  03452dd   Add sections on dependencies and making configure to the INSTALL file.
       new  078069b   Travis updates.
       new  5c695a1   Prevent infinite loop on empty indexes
       new  ca1423d   Fix over-specified location of htslib.pc.tmp
       new  d2d9c76   Release 1.4: summary
       new  0172fe3   Merge tag '1.4' into debian/unstable
       new  94d9711   New upstream version
       new  e742362   Update patches
       new  46d5eee   Drop autoconf from Build-Depends, add libbz2-dev and liblzma-dev to Build-Depends

The 123 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:
 .gitignore                                     |   13 +
 .travis.yml                                    |   23 +-
 INSTALL                                        |  104 +-
 Makefile                                       |  247 +++--
 NEWS                                           |   89 ++
 README.md                                      |    5 +-
 bcf_sr_sort.c                                  |  645 +++++++++++
 bcf_sr_sort.h                                  |  103 ++
 bgzf.c                                         | 1250 +++++++++++++++------
 bgzip.c                                        |   38 +-
 config.h.in                                    |   38 -
 config.mk.in                                   |   56 +-
 configure.ac                                   |  243 ++++-
 cram/cram_codecs.c                             |  180 +++-
 cram/cram_codecs.h                             |    4 +
 cram/cram_decode.c                             |  182 +++-
 cram/cram_encode.c                             |  904 +++++++++-------
 cram/cram_encode.h                             |   10 +
 cram/cram_external.c                           |   16 +
 cram/cram_index.c                              |  134 +--
 cram/cram_index.h                              |    4 +-
 cram/cram_io.c                                 |  331 ++++--
 cram/cram_io.h                                 |   79 +-
 cram/cram_samtools.c                           |   15 +-
 cram/cram_samtools.h                           |    2 +-
 cram/cram_stats.c                              |  266 +----
 cram/cram_structs.h                            |   57 +-
 cram/open_trace_file.c                         |    1 -
 cram/os.h                                      |   96 +-
 cram/pooled_alloc.h                            |    2 +
 cram/rANS_byte.h                               |   14 +
 cram/rANS_static.c                             |  200 ++--
 cram/sam_header.c                              |    5 +-
 cram/string_alloc.c                            |    2 +-
 cram/thread_pool.c                             |  757 -------------
 cram/thread_pool.h                             |  218 ----
 cram/vlen.h                                    |    2 +
 cram/zfio.c                                    |   41 +-
 debian/changelog                               |    8 +
 debian/control                                 |    3 +-
 debian/patches/define_PATH_MAX.patch           |   10 +-
 debian/patches/fix_pkg-config.patch            |    8 +-
 errmod.c                                       |  194 ++++
 faidx.c                                        |  334 +++---
 hfile.c                                        |  242 ++++-
 hfile_gcs.c                                    |  137 +++
 hfile_internal.h                               |   25 +-
 hfile_irods.c                                  |  259 -----
 hfile_libcurl.c                                |  459 ++------
 hfile_s3.c                                     |  400 +++++++
 hts.c                                          |  573 +++++++---
 hts_internal.h                                 |   96 ++
 htsfile.1                                      |    9 +-
 htsfile.c                                      |  191 ++--
 htslib.mk                                      |   24 +-
 htslib.pc.in                                   |   15 +-
 htslib/bgzf.h                                  |  106 +-
 htslib/cram.h                                  |   37 +-
 htslib/faidx.h                                 |  188 ++--
 htslib/hfile.h                                 |  190 ++--
 htslib/hts.h                                   |  194 +++-
 htslib/hts_defs.h                              |    8 +-
 htslib/hts_endian.h                            |  354 ++++++
 htslib/knetfile.h                              |    1 +
 htslib/ksort.h                                 |    3 +-
 htslib/kstring.h                               |   99 +-
 htslib/regidx.h                                |    2 +
 htslib/sam.h                                   |  178 ++-
 htslib/synced_bcf_reader.h                     |   59 +-
 htslib/tbx.h                                   |    9 +-
 htslib/thread_pool.h                           |  290 +++++
 htslib/vcf.h                                   |  108 +-
 htslib/vcf_sweep.h                             |    5 +-
 htslib/vcfutils.h                              |   14 +-
 htslib_vars.mk                                 |    6 +-
 knetfile.c                                     |    6 +-
 kstring.c                                      |  124 ++-
 md5.c                                          |    3 +-
 multipart.c                                    |  242 +++++
 plugin.c                                       |   10 +-
 probaln.c                                      |  285 +++++
 realn.c                                        |  199 ++++
 regidx.c                                       |   15 +-
 sam.c                                          |  620 ++++++++---
 synced_bcf_reader.c                            |  242 ++---
 tabix.1                                        |   14 +-
 tabix.c                                        |   48 +-
 tbx.c                                          |   88 +-
 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                            |   22 +-
 test/cross_validate.sh                         |    4 +-
 test/{formatcols.vcf => formatmissing-out.vcf} |    2 +-
 test/{formatcols.vcf => formatmissing.vcf}     |    2 +-
 test/hfile.c                                   |   44 +-
 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                       |  182 ++++
 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                            |  546 ++++++++++
 test/test-regidx.c                             |   10 +-
 test/test.pl                                   |   89 +-
 test/test_bgzf.c                               |  789 ++++++++++++++
 test/test_view.c                               |   21 +-
 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                                  | 1376 ++++++++++++++++++++++++
 thread_pool_internal.h                         |  165 +++
 vcf.c                                          |  596 +++++++---
 vcf_sweep.c                                    |    4 +-
 vcfutils.c                                     |  218 +++-
 134 files changed, 14337 insertions(+), 4816 deletions(-)
 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
 create mode 100644 errmod.c
 create mode 100644 hfile_gcs.c
 delete mode 100644 hfile_irods.c
 create mode 100644 hfile_s3.c
 create mode 100644 htslib/hts_endian.h
 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_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

-- 
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