[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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