[med-svn] [htslib] annotated tag 1.2 created (now 38563fc)
Charles Plessy
plessy at moszumanska.debian.org
Mon May 25 02:39:00 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag 1.2
in repository htslib.
at 38563fc (tag)
tagging bff5efb85c581efc42d9f3483aa919161906ad0a (commit)
replaces 1.1
tagged by John Marshall
on Mon Feb 2 14:53:12 2015 +0000
- Log -----------------------------------------------------------------
HTSlib release 1.2, CRAM and format detection improvements
David Roazen (1):
bcf_sr_add_reader(): do not increment nreaders or perform any reallocs upon file open errors
James Bonfield (72):
Minor speed increases to cram_byte_array_stop_decode_init and
Added a range coder (order 0 and 1) plus support for LZMA if compiled
Tweaks for specifying version number. Now accepting version 3.0, and
Updated the version checks to lop off major/minor components rather
Fixed BETA codec so that it honours beta offset value for zero length
Bug fix to the external decoders. If there is an attempt to decode 0
Added support for more codecs, as part of refactoring how data is
Major refactoring of the way CRAM handles external blocks.
Removal of a couple memory leaks added in the restructing of the last
Bug fix of use of TAG_ID macro and k vs key in hash for auxiliary
Modified the thread pool to use as few threads as possible. The
Bug fixed scramble -x as it was not correctly setting the RI data
A mishmash of changes for CRAM v3.0 (not yet the default output
Minor gcc warnings fixups.
Added support for compressed SAM headers.
Final part of Staden io_lib's commit r3686.
Initialise refs_t ->ref_id in refs_load_fai(). This has no bearing on
Added CRC32 to the blocks and containers.
Fixed the file format detection code so it handles CRAM v3.0 magic
Changed the hts_open code to support "C" as a format mode as well as
Fixed bam_construct_seq to cope with qual being NULL.
Removed the previous "c" vs "C" hack and added a proper option parser
Fixed generation of MD and NM tags in cram_decode_seq() when using a
Added a special case for setting the reference. When converting from
Cope with cram_compress_slice failing. We were unwinding the stack
Removed the need for -DSAMTOOLS when compiling CRAM.
(Commented out): ugly auto-configuration of HAVE_LIBBZ2 and
Added multi-threading support for reading and writing CRAM.
CRAM_OPT_VERSION now works (and only works) on an open file
Added SAM_RGAUX as another column identifier to allow for tools that
Removed defunct comment.
Minor tidyups to prevent some clang warnings.
Fixes for handling range requests while also multi-threading.
Fix for FSECONDARY reads; do not link into PNEXT/RNEXT.
Removed various small memory leaks.
Split off the rans_byte.h portion of rANS_static.c back into its own
Added copyright notice.
Amended the compression level checking code in cram_dopen() to follow
In a bid to keep the DEBUG_printf line potentially printing up the
Fix a bug where hts_set_fai_filename() didn't pass this through to
Fix bug spotted by valgrind when running "./test_view -D
Fixed an error found via valgrind of test_view -D c1#pad1.tmp.cram.
Reverting 9e844e0be26875d29b6e2c853c2b4d02c4f1faa4 and rewriting in a
Sped up cram_index_load some 200 fold by replacing sscanf with our own
Fixed an incorrect EOF-style case when seeking multiple times.
Amended/removed comments about scram_* API.
Fixed the generation of read names to use record_counter properly,
Replaced sprintf with a home-brew append_uint64 function. This is a
Minor improvement to binary searching in CRAM indices.
Removed spurious messages about missing EOF blocks in CRAM when
Added in the compressed length field to the rANS codec header.
Two changes to cram_encode_container() related to efficient encoding
Fixed a memory leak when destroying a BYTE_ARRAY_LEN encoder.
Fixed a small memory leak where we didn't deallocate a cram_block that
Fixed memory leak when trying to O1 compress a block <= 4 bytes long.
Make the multi_seq parameter default to auto. This is the default in
More ref and memory management fixes.
Reverted the cram_encode_container change to call cram_ref_incr and
Merge pull request #160 from jkbonfield/fix_unsorted_cram
Fixed a bogus warning about using 'cp' before initialised. (Bogus as
Minor change to allow REQUIRED_FIELDS option to be specified in hex or
Overhauled the cram_dependent_data_series function and associated
Fixes imported from Staden io_lib revisions 3792/3795.
Enforce the use of a local cache (use home dir if not defined)
Use TMPDIR and if not set TEMP (common on Windows) environment
Stylistic code change: !*ptr vs *ptr=='\0'.
Additional comments.
Merge pull request #161 from jkbonfield/cram_dependent_data_series
Fixed unnecessary FAI building.
Bug fix to refs_from_header().
Improved the CRAM stats array usage.
Added support for XDG_CACHE_HOME.
John Marshall (43):
Merge version number bump from master
Formatting fixes for man page
Fix regidx.o dependencies and htslib.mk; alphabetise
Merge man page formatting fixes
Remove -DSAMTOOLS vestiges
Fix cram/rANS_* dependencies
Merge CRAM v3 updates (PR #132)
Add htsFormat and format-detection API functions
Use htsFormat to replace htsFile's is_foo flags
Add htsfile utility
Merge origin/develop, replacing htsFile.type by .format
Parse SAM aux 'i' values > 2^31 correctly
Fix compilation when ALLOW_UAC is not defined
Merge short read() bug fix from upstream
Fix ks_getuntil2() extra empty record at EOF bug
Add seq_nt16_int[], equivalent to the old API's bam_nt16_nt4_table[]
Account for read buffering in hseek(SEEK_CUR)
Sanity-check tid in hts_itr_query()
Parse regions without begin/end as 1..MAX_INT rather than 1..2^29
Update khash.h from upstream sources
Fix various simple memory leaks (cf #138)
Deobfuscate memory allocations etc via sizeof()
Avoid aux.* filenames, which are invalid on Windows
Add iRODS hFILE backend
Add MIT/Expat license boilerplate
Add configure.ac script
Add notes for building from a Git repository
Merge iRODS hFILE backend
Document ./configure --with-irods
Add hisremote(), and convert faidx.c from knet to hFILE
Set resource when writing to iRODS
Add htsfile(1) man page
Remove tabix -i, which duplicates htsfile functionality
Detect file format versions in hts_detect_format()
Temporarily avoid rcDataObjFsync() [workaround]
Merge CRAM TLEN updates (PR #165)
Avoid hiding under .cache in temp directories
Merge default local reference cache (PR #166)
Rationalise include guard macro name
Move remainder of config.h to bgzf.c and remove it
Reinstate faidx_fetch_nseq() alongside faidx_nseq()
Formatting fix for HTML man page
Release 1.2: various bug fixes, htsfile utility, CRAM improvements, etc
Martin O. Pollard (1):
Fix comment in sam.h
Matt Shirley (1):
Update faidx.h
Petr Danecek (35):
bgzf_open(..,"g") for compressed gzip output, as opposed to BGZF
Added regidx API which should replace bcf_sr_regions at some point
Clean after regidx init failure; fixed build dependencies
Fix in bcf regions which in some situations would skip first
regidx: simple file format autodetection
Return type of bgzf_getc is int, not char
regidx: use size_t, not ssize_t
Support for Type=Character, in htslib same as Type=String
VCF header editing speedup for large number of ref sequences
New bcf_copy API
Removed old hts_file_type() API and replaced it with the new htsFormat;
Clean up, is_compressed and is_cram no longer necessary
Do not use 0x80 & co for missing alleles
Do not load remote index if already exists locally
Fix in bgzf's gzip reading plus added a test for this
bcf_translate: Be aware of gaps in BCF headers
tbx: Detect faulty tbi files
Fix of memmove bug in bcf_remove_filter()
bcf_sr_get_header() macro for accessing the synced readers' headers
Add IDX to hdr tags of different type, fixes issue https://github.com/samtools/bcftools/issues/141
bcf_hdr_subset: Return NULL on duplicate sample names
Sanity check to detect broken GT fields in bcf_calc_ac()
bcf_*hrec* functions: check for existing/multiple IDX keys
vcf: skip empty INFO tags ";;". (Error might be more appropriate?)
bcf_hdr_combine: Complain when trying to merge different types
bcf_calc_ac: Check for incorrect AC/AN counts
vcf_parse_format: Throw an error on extra FORMAT fields
vcf: Propagate hdr_add_sample() error
Fix alleles trimming with format Number=R/A/G tags
vcf headers: Allow contig lines without length attribute. Resolves #155
tabix: Remove bcf and bam from presets,
vcf: Abort on duplicate sample names, resolves #184
New -R/-T options to tabix.
Fix a typo, VCF contig length should be stored.
Better index bugfix
Shane McCarthy (1):
add new test-regidx binary to .gitignore
pd3 (3):
Merge pull request #136 from mcshane/feature/ignore_test-regidx
Merge pull request #142 from reinders/patch-1
Merge pull request #144 from broadinstitute/broad_bcf_sr_add_reader_segfault_fix
reinders (1):
Buffer overflow error in synced_bcf_reader.c
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