[med-svn] [htslib] branch master updated (2064848 -> 50db54b)

Andreas Tille tille at debian.org
Fri Nov 4 11:54:04 UTC 2016


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

tille pushed a change to branch master
in repository htslib.

      from  2064848   Merge version number bump and NEWS file from master
       new  9919fca   Use internal plain char isdigit_c()/etc ctype functions
       new  d8c1ca3   Removed use of CRAM "CORE" block while encoding.
       new  543f030   Add {errmod,kprobaln,bam_md}.[ch] from samtools
       new  96acc6c   Retain only library parts of realn.c; canonicalise whitespace
       new  55b2ae4   Add errmod declarations to htslib/hts.h and errmod.o to Makefile
       new  1e6909b   Rename kpa_glocal() to probaln_glocal() and add to htslib/hts.h
       new  8439061   Rename as sam_cap_mapq()/sam_prob_realn() and add to htslib/sam.h
       new  622bfaa   Remove probaln_par_def/probaln_par_alt constants
       new  b183ab2   Add errmod / probaln / prob_realn to HTSlib API (PR #343)
       new  10e3c2c   Remove unused variable [minor]
       new  0454d47   Fix len parameter type [minor]
       new  6d70a0e   Create API to check EOF on all htsFile that support EOF block
       new  f2399ee   New bam_mplp_reset function to allow mplp in multiple regions
       new  cd2d915   Fix potential infinite loop [minor]
       new  1385d7a   Replace bcf_hdr_fmt_text(), which can't handle huge headers
       new  cb92f20   Read BCF header's l_text as unsigned
       new  f581de8   Merge fixes for huge BCF headers (PR #373)
       new  1cc7d12   Add curl_kput(), which slurps an URL into a kstring
       new  fc062fb   knetfile.c: Only emit Range header if needed
       new  b64e076   Make hts_itr_query find no-coor reads when last reference is unused.
       new  ab793a8   Don't assume order of sequence_ids when finding HTS_IDX_NOCOOR location.
       new  375ba53   Merge hts_itr_query(HTS_IDX_NOCOOR) fixes (PR #376)
       new  e5ab997   Fixed out by one error in bin calculation (CRAM -> BAM).
       new  21e6a8f   Reorder Makefile dependencies [minor]
       new  abfd337   Use internal plain char isdigit_c()/etc ctype functions
       new  5720e3e   Deleted the broken code in zfopen() when HAVE_POPEN is defined.
       new  e1dd635   Sam_index_build(2) now returns -4 for failure to save/create the index.
       new  43a94fb   Write CRAM ref cache via hFILE rather than stdio
       new  bb03b02   Added bam_aux_update_str()
       new  f58922d   Add doxygen @file documentation
       new  4eef9a7   Fixed CRAM MD/NM generation to follow the same logic as calmd.
       new  67234cb   Make kstring detect more errors and work better on 64 bit systems
       new  02220bf   Use hts_get_bgzfp() when format.compression==bgzf
       new  481752c   Not with tabs, James! [minor]
       new  11661a5   Show coordinates in "unsorted positions" error message
       new  4b1610f   Added a lossy read-name option (CRAM_OPT_LOSSY_NAME).
       new  4c0b93b   Made the CRAM_OPT_PREFIX option external via the "name_prefix" option.
       new  f689e18   Merge CRAM lossy name compression (PR #326)
       new  53b5f5d   Expose cram_get_refs() function to return the opaque refs_t data type.
       new  d496268   allow bcf_index_build2 to index both bcf and vcf
       new  b6aa0e6   Detect shared library and plugin types during configure
       new  3f41083   stringify_argv(): suppress trailing space
       new  1eec11b   Fixes bug in bam_aux_update_str()
       new  2cddfb3   Build DLL and plugins on Cygwin
       new  3a8d3d3   Htslib now copes with zero length Z and H aux tags.
       new  4502742   Use hFILE rather than stdio when reading indices
       new  1c6cf22   Fixed file-descriptor leak in refs_load_fai().
       new  925a3c9   Document required Cygwin (and RPM-style) devel packages
       new  02e9d21   Add is_cram flag to distinguish dummy hts_itr_t objects
       new  155e1aa   Add print-config target
       new  0de7fe5   Generate config.h.in with autoheader
       new  86260e1   Add configure check for fdatasync()
       new  c6cb4c3   Use finer-grained $(INSTALL_LIB) and $(INSTALL_MAN) macros
       new  5869a67   hts_itr_query(): discard chunks far beyond the query region
       new  0d5a5eb   Avoid linguist mis-classification [minor]
       new  fd721f1   Allocate BGZF::uncompressed_block/compressed_block together
       new  344c825   Allow plugins to select RTLD_LOCAL or RTLD_GLOBAL
       new  0f2a88a   Protect against sequences starting beyond reference end.
       new  e8bddbe   Use native Doxygen API documentation markup
       new  e87ae87   Add interfaces to hfile for delimited string input
       new  ed502be   [faidx.h] Use native Doxygen API documentation markup
       new  f86372e   Remove iRODS plugin, which has moved to samtools/htslib-plugins
       new  74bcfd7   Embed version number directly in hfile_libcurl plugin
       new  23d7f17   Discard distant chunks based on binning index, not linear index
       new  bbaab35   [tabix man page] Note coordinate arguments are 1-based inclusive
       new  c31216b   Added bgzf_block_write() and rebgzip option. Check indexing and rebgzip are not attempted simultaneously.
       new  eaef296   Added bgzip test files. Add bgzip --rebzip test and update test files.
       new  54dc232   Rebased PR#387 and minor code formatting fixes (trailing white space, indentation, tabs) for consistency with existing code.
       new  e79775f   Added bgzip to check/test dependency.
       new  71db687   Treat regions [-1,n) as [0,n) when indexing
       new  8d957c0   Rewrite #ifdeffed-out use of now-removed variable [minor]
       new  9c230e7   Fixed out by one error in bin calculation (CRAM -> BAM).
       new  ebdb5aa   Allow plugins to select RTLD_LOCAL or RTLD_GLOBAL
       new  5586168   Provide a fallback for PATH_MAX if it is not defined
       new  6bed35a   Release 1.3.2: bin field bug fix, RTLD_GLOBAL plugins
       new  503b09d   Merge version number bump and NEWS file from master
       new  bdf85e4   Speed up to probaln_glocal.
       new  88517df   Added callback + client data hooks to pileup iterators and pileup struct.
       new  3566540   Factored in the renormalisation to the f[] computation.
       new  8c595df   Cosmetic: 0 to NULL
       new  f10f9b2   Bump SOVERSION to 2 and note ABI incompatibility in NEWS
       new  bf75336   Merge (ABI-changing!) mpileup callbacks (PR #398)
       new  0ca17a0   Handle VCF lines with misssing `FORMAT=.`
       new  19c1894   Fix bugs in bam_aux_update_str()
       new  4295de4   Bug fix: 0 is a valid return value of bcf_hrec_find_key
       new  553406d   Use <inttypes.h> instead of old WIN32-specific code
       new  519f75a   Prompoted cram/thread_pool code to the top-level and use it within bgzf writing instead of its own multi-threading.
       new  aaf998a   Tidied up the mass of #ifdefs.
       new  f72add4   Further updates to multi-threading.
       new  2cb33f9   Fixed dependencies & .mk defs so Samtools links too (threading change).
       new  70f1fae   Fixed uninitialised memory (queue shutdown).
       new  242e03e   Tidied up pointless while/if duplication. (Left over from a more complex structure.)
       new  6717817   Draft of the multi-threaded decoder.
       new  2ef8e3e   Committing as it's a working MT decoder now.
       new  41a714a   Attempt to use shared pool.
       new  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.
       new  5142d24   Bumped the sample size for the tests, and made all tests share a common size.
       new  8e9bd80   White space updates (tabs -> spaces).
       new  7d50ac6   Sorry, updates to the previous commits too; forgetting to add this file!
       new  0ba5636   Updates to cope with the new thread pool API.
       new  2af39f8   Removed some debugging and changed the default queue sizes to be smaller.
       new  bd32ec6   Improvements to avoid boom & bust scenarios.
       new  8a8fac2   Culled the duplicate is_compressed assignment.
       new  2c2330b   Various memory leaks fixed in bgzf multi-threading.
       new  bedeccc   First apparent working bgzf_seek implementation.
       new  d6dacc7   Added HTS_OPT_CACHE_SIZE option to specify the bgzf cache size.  This can speed up decoding considerably in certain circumstances.
       new  f522f1f   Made thread job serial numbers 64-bit.
       new  15ef81b   Improvements to multi-threading encode/decode/transcode.
       new  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.
       new  c721a74   bgzf_check_EOF now works when input is multi-threaded.
       new  9d2e3de   Propagate read error in thread breader ack to fp->errcode error in main thread.
       new  511a235   Deleted the now defunct read_eof variable.
       new  d0614e5   Fixed bgzf_getc and bgzf_getline to work in multi-threaded mode.
       new  8ca0175   Added support for multi-threaded BAM indexing.
       new  e65f67d   Fixed CRAM_OPT_THREAD_POOL for cram.
       new  173a5d0   Merge branch 'develop' of https://github.com/samtools/htslib into threading_pool
       new  93be96b   Bug fix to hts_get_bgzfp.
       new  d365af3   Improvements for VCF/BCF multi-threading.
       new  ccd48bd   Make sure we destroy the thread_pool when created by ourselves.
       new  eceeb01   Merge branch 'develop' of https://github.com/samtools/htslib into threading_pool
       new  3ade6b6   Bug fix to bgzf_read, which was breaking samtools index (and more).
       new  4f29e22   PTHREAD_MUTEX_RECURSIVE_NP vs PTHREAD_MUTEX_RECURSIVE.
       new  7235947   Code tidyup.
       new  1659e8f   test_view now also verified multi-threading.
       new  cc4fe23   Removal of debugging output.
       new  3bfd281   Migrated the thread pool structures to thread_pool_internal.h.
       new  c00fe2c   Renamed various thread pool structs/functions.
       new  299c7b6   Culled the DEBUG_TIME code in thread_pool.
       new  5c59172   Further tidying up of queue vs process; mostly comments and docs.
       new  3d3cc32   Fixed a race condition in the multi-threaded cram encoder.
       new  5b31094   Fixed a double free in multi-threaded CRAM and regions.
       new  b077a6b   Replaced BSD license with MIT license for consistency.
       new  7a54ff9   Avoid extraneous #includes
       new  daae2ea   Merge threading pool API (PR #397)
       new  d58eab8   Fix error handling in cram_index_load.
       new  6ff0ca0   Don't redefine thread_pool.h typedefs
       new  609120d   More thorough INFO cleaning to prevent issues like https://github.com/samtools/bcftools/issues/428
       new  f7370bb   Activate auxf#values_java.cram test
       new  1bc5c56   Ensure headers compile by themselves [minor]
       new  50db54b   Suppress index date warning when hts_verbose == 0

The 140 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                                     |    5 +
 INSTALL                                        |   18 +-
 Makefile                                       |   92 +-
 NEWS                                           |   24 +-
 README.md                                      |    5 +-
 bgzf.c                                         |  770 +++++++++++---
 bgzip.c                                        |   34 +-
 config.h.in                                    |   38 -
 config.mk.in                                   |   42 +-
 configure.ac                                   |   88 +-
 cram/cram_decode.c                             |  101 +-
 cram/cram_encode.c                             |  268 ++++-
 cram/cram_encode.h                             |   10 +
 cram/cram_external.c                           |   16 +
 cram/cram_index.c                              |  134 +--
 cram/cram_index.h                              |    4 +-
 cram/cram_io.c                                 |  171 ++-
 cram/cram_samtools.c                           |    2 +-
 cram/cram_stats.c                              |  266 +----
 cram/cram_structs.h                            |   10 +-
 cram/open_trace_file.c                         |    1 -
 cram/pooled_alloc.h                            |    2 +
 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 +-
 errmod.c                                       |  194 ++++
 faidx.c                                        |   30 +-
 hfile.c                                        |   73 +-
 hfile_internal.h                               |    1 -
 hfile_irods.c                                  |  259 -----
 hfile_libcurl.c                                |   74 +-
 hts.c                                          |  153 ++-
 htsfile.1                                      |    2 +-
 htslib.mk                                      |    8 +-
 htslib/bgzf.h                                  |   34 +-
 htslib/cram.h                                  |   37 +-
 htslib/faidx.h                                 |  151 ++-
 htslib/hfile.h                                 |  185 ++--
 htslib/hts.h                                   |   91 +-
 htslib/knetfile.h                              |    1 +
 htslib/ksort.h                                 |    3 +-
 htslib/kstring.h                               |   98 +-
 htslib/regidx.h                                |    2 +
 htslib/sam.h                                   |   57 +-
 htslib/synced_bcf_reader.h                     |   21 +-
 htslib/tbx.h                                   |    7 +-
 htslib/thread_pool.h                           |  281 +++++
 htslib/vcf.h                                   |   65 +-
 htslib/vcf_sweep.h                             |    5 +-
 htslib/vcfutils.h                              |    5 +-
 htslib_vars.mk                                 |    1 +
 knetfile.c                                     |    2 +-
 kstring.c                                      |   10 +-
 plugin.c                                       |   34 +-
 probaln.c                                      |  285 +++++
 realn.c                                        |  199 ++++
 regidx.c                                       |    9 +-
 sam.c                                          |  109 +-
 synced_bcf_reader.c                            |   39 +-
 tabix.1                                        |   14 +-
 tbx.c                                          |   16 +-
 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                                   |   10 +-
 test/md#1.sam                                  |   12 +
 test/md.fa                                     |    3 +
 test/md.fa.fai                                 |    1 +
 test/sam.c                                     |   12 +-
 test/test-regidx.c                             |   10 +-
 test/test.pl                                   |   69 +-
 test/test_view.c                               |   20 +-
 thread_pool.c                                  | 1350 ++++++++++++++++++++++++
 thread_pool_internal.h                         |  165 +++
 vcf.c                                          |  176 +--
 85 files changed, 5001 insertions(+), 2543 deletions(-)
 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
 delete mode 100644 hfile_irods.c
 create mode 100644 htslib/thread_pool.h
 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/md#1.sam
 create mode 100644 test/md.fa
 create mode 100644 test/md.fa.fai
 create mode 100644 thread_pool.c
 create mode 100644 thread_pool_internal.h

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