[med-svn] samtools annotated tag 0.2.0-rc8 created (now 16d7eac)
Charles Plessy
plessy at moszumanska.debian.org
Mon Aug 18 01:39:59 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag 0.2.0-rc8
in repository samtools.
at 16d7eac (tag)
tagging 16b3d9c4eb1999d9baba0b93a7582678a36c5475 (commit)
replaces 0.2.0-rc7
tagged by John Marshall
on Thu May 8 17:06:00 2014 +0100
- Log -----------------------------------------------------------------
Test release RC8
Erik Aronesty (1):
add -U FILE to output unselected reads for pipelin
James Bonfield (2):
Added mpileup tests
Mpileup test in Makefile
John Marshall (38):
Extant code in sam_view.c does not use Yoda conditions
Merge read group filtering changes (PR #164)
Print dummy column for MAPQ for mpileup -s
Disconnect clean-htslib from clean target
Don't malloc the kstring_t; minor changes to the big comment
Merge BED file parsing improvements (PR #165)
Merge view -U option (PR #177), also adding it to the man page
Merge view subsampling randomness (PR #167, fixes #160)
Merge test cases from Rob Davies (PR #162)
Make xfail/xpass useable by other test subroutines
Make test_view() -@ tests portable to OS X
Don't require an index for full-file merges
Merge branch 'origin/develop' into develop
The @HD header is optional
Add "make testclean" target
Make stats.c's error() static like the others
Add print_error() and print_error_errno()
Merge BED file option error checking (PR #77)
Move CDF_MWU_TESTS switch closer to what it controls
Fix dependencies for test/test.h
Write files based on the *basename* of the input file
Reinstate old-API functions needed by Bio-SamTools Perl module
bam_dup1() is now provided by htslib
Merge phase.c htslibification (PR #190)
Merge blast2sam.pl improvements (PR #114)
Silence -Wstrict-prototypes warnings
Merge split subcommand (PR #172)
Revert mpileup long options changes
Avoid bashisms
Abort if an INIT command fails; dispose of _out file
Testclean and ignore temporary and output files
Use hts_set_threads() rather than bgzf_mt()
Report sam_write1() and sam_close() errors
Merge mpileup tests (PR #187)
Fix long option has_arg inconsistencies
Use kstring instead of POSIX 2008's strndup()
Merge split cleanups (PR #210)
Remove our bgzip.c in favour of htslib/bgzip
Martin O. Pollard (15):
Convert samtools stats to htslib
Add Test files for stats
Fix compiler warning in stats
Enable tests for samtools stats
Create header of common test functions
Add split command to samtools
Add unit test for bam_split.c's count_rg
Polish bam_split
Add unit test for bam_split.c's filter_header_rg
Restructure testing structure to dedupe
Add unit test for bam_split.c's parse_args
Further stats tests
Convert phase to htslib API
Clean up merge memleaks
Cleanup split memleaks
Nicholas Clarke (3):
Adds support for outputting stats over the full input size distribution.
Remove unusued 'total' functions.
Fixes an issue with -i0 involving truncation of insert sizes.
Petr Danecek (14):
view: Free the header once finished
merge,sort: Output BAM, not SAM. Build indexes
plot-bamstats: Fixes #183
Support for =X cigars in mpileup, exit on yet untreated cigars.
Free all memory in sparse_isize_free
stats: Support for =X cigars
Added expected outputs for stats tests
stats: Prevent nan on output
mpileup: Long options; Custom DP,DV,DP,DP4 format fields on output
Removed debugging exit in test.pl; Updated excl/incl long opts
mpileup opts: -1,2 now recognised, --ff,rf on popular demand back
mpileup opts: Added forgotten --ff
For your amusement, --ff goes with -2
mpileup: Absolute INFO/QS to allow incremental calling
Rob Davies (33):
Adds *~ (emacs backup files) and core to .gitignore.
Adds tests for samtools view.
Merge branch 'develop' into develop_testing
Turns on CRAM region tests, now that CRAM indexing is supported.
Adds -L (BED file reading) tests.
Adds tests for the -t, -T and -B options.
Adds more region tests.
Rolls converting back to SAM into run_view_test
Adds CRAM conversion using the MD5 REF_CACHE.
Merge branch 'develop' into develop_testing
Strips out -x / -X tests as -X is deprecated and -x has been repurposed.
Adds more optional fields in test file, and more -R / -r checks.
Adds tests for the new -x tag stripping option.
Adds tests for currently undocumented -m and -Q options.
Adds some unaligned reads to the samtools view test file.
Minor changes to samtools view test output file names.
Adds tests for the -s (subsampling) and -@ (threads) options
Makes filter_sam filter @RG lines when filtering by read group.
Adds comments to explain how the samtools view testing functions work.
Changes *_compare functions to not call passed() or failed().
Removes dependency on gunzip
Merge branch 'develop' into develop_testing
Adds tests for 'samtools cat'
Makes -r and -R read group filtering options both use settings.rghash
Adds more optional tags to alignment lines.
Rewrite bed_read
Adds check to ensure bed_read worked, and exits non-zero if not.
Stops samtools view from writing unmapped reads with -L (BED file) option
Ensures non-zero exit if -r / -R options fail to work.
Makes samtools view subsampling option more random.
Add tests for bam2fq.
Adds tests for samtools depad.
Adds expected fail and unexpected pass.
Shane McCarthy (1):
fall over if a bed file given as an option cannot be read
pd3 (4):
Merge pull request #174 from mp15/stats
Merge pull request #179 from mp15/stats
Merge pull request #184 from wtsi-hgi/features/unbounded-is
Merge pull request #186 from wtsi-hgi/issues/warn-unusued-fn
pruzanov (2):
Fixed script for parsing BLAST output
Fixed a few bugs in blast2sam.pl script, added POD documentation
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