[med-svn] samtools annotated tag 0.2.0-rc1 created (now e162377)
Charles Plessy
plessy at moszumanska.debian.org
Tue Dec 10 10:06:32 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag 0.2.0-rc1
in repository samtools.
at e162377 (tag)
tagging b294a1b363aea261f08297ad736aab841f4762d1 (commit)
replaces 0.1.19
tagged by John Marshall
on Mon Oct 21 17:10:27 2013 +0100
- Log -----------------------------------------------------------------
Test release RC1
Brent Pedersen (1):
use or on the -F and -f flags so that multiple flags can be specified from the command-line.
Hanspeter Niederstrasser (1):
Add generated files to .gitignore
John Marshall (40):
Merge pull request #50 from mp15/char_array
Merge pull request #53 from brentp/or_flags
Merge trivial changes from htslib's knetfile.c
Use htslib's klib instead of our own
Use htslib's bgzf.h, faidx.h, and razf.h
Ensure examples/calDepth compiles
Use all-bgzf_*() functions instead of a mixture
bamshuf.c already uses the htslib API
Use the generic bam_write1() here
Remove bam_nt16_nt4_table from the public header
Call bam_remove_B() explicitly
Temporarily comment out header manipulation
Replace libbam with htslib API wrappers
Move bam_fetch() to libbam's bam.c
Add Travis CI control file
Ensure travis's $(CC) overrides our Makefile's
Fix thinko: a shell variable, not a make variable
Merge branch 'develop' into with-htslib
Include htslib in our build directory
Include htslib rules and add header dependencies
Fix buglet: initialise the kstring_t
Warn and use correct bin when bin field is wrong
Fix bin calculation for unmapped reads
Revert prematurely-committed bam_pileup work
Set samtools sort's exit status from errors
Fix samtools sort -f temporary file names
Updates for recent htslib changes (9dfcc31)
Merge branch 'with-htslib' into develop
Remove recursive make for "misc" subdirectory
Tidy up makefile
Fix typo, remove razip vestige [minor]
Also run our tests
Set Git attributes for BAM files in the repository
Add help command and --version options
Write samtools --help output to stdout
Ensure $HTSDIR is used by "make test" too
Remove bcftools, SAM, and VCF sections from man page
Detect input format and add samtools view -C option
Add "make install" target
Add omitted non-Perl misc/ programs
Martin Pollard (13):
Changed code where variable used for getopt is then reused by later code for completely different purpose.
razf_read and razf_write are intended to replace system calls of read and write respectively and thus their method signature should match.
Tweak method definitions of knet_read and knet_write to better match system read and write.
Add const modifier to certain global constants.
Adjust position of fileret in _razf_read and ensure correct variable is returned.
Fix bgzf read and write prototypes to better match system ones, length is size_t not ssize_t
Add comments, make variable names more meaningful and clean up a few things in bcftools (including some spaces that crept in that should have been tabs).
Use off_t and lseek rather than the 64 alternatives as this is more portable.
Fix signed return going into unsigned variable
Cleanup and add comments to genotype calling code
Follow per-file convention for using either tabs or spaces
Convert from const char* to const char[]
Fix whitespace inconsistancy and add license to bam_tview.c.
Petr Danecek (50):
mpileup fix: Print error message and exit when no files given. (On behalf of Gert Hulselmans)
mpileup indel hotfix: fix in detecting long stretches of N's. The version string can be now overriden, either directly or using git-stamp Makefile rule
The indel stats (IS) annotation splitted into two: IDV and IMF
bgzip now compiles
bcftools: more informative error message, print position of the bad site
Added a few comments.
mpileup now handles overlapping reads, not counting the overlaps twice. This is a largely untested, backup commit.
mpileup: overlap soft-clipping moved out of user space (mplp_init) into plp core library, otherwise first pair is not accesible for clipping
plot-bamcheck: New -m option for merging multiple bamcheck files. All sections except GC-by-depth.
mpileup (overlapping reads, continued): Instead of soft-clipping the first read, set quality of conflicting bases to 0. Include command line in VCF header.
mpileup (overlapping reads, continued): fixed a bug, check a single base, not multiple
This is a broken version: backup commit
Fix in kt_fisher_exact: prevent infinite loops. Speed up call_multiallelic_gt for ref-only sites. Cleaned overlap code in bam_pileup.c
Merge remote branch 'origin/master' into develop
bam_pileup.c: Skip unpaired reads or reads with unmapped mates.
samtools mpileup/bcftools view: Fix of integer overflow at very high depths with many samples. Added MQ0 annotation.
bcftools view -m: Output only alleles which are actually used in GTs, even if the LRT has chosen a wider set, as this is less confusing. Note that the original version neglected to add zero values into the AC vector.
Correct initialization of the anno16 double version. Prevent output of multiple semicolons in VCF INFO field.
bcftools view: Fixed a memory leak and a bug introduced in commit 22904640 which caused that hom AA calls were not reported.
mpileup: Initialize properly the MQ0 annotation
bcftools view: Output CLR,UGT,CGT tags in -m pair/trio calling. In this version, consistency with output genotypes is not being checked.
bcftools view: prevent segfault when running in plain mode, p1 then does not exist
bcftools view: previous fix in kt_fisher_exact (PV4 annotations, fet.c) was wrong. Will this one work better?
Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
Added a test suite for samtools, currently faidx and bgzip are tested.
Added a test suite for samtools, currently faidx and bgzip are tested.
tview and bgzip: Check that the files are bgzipped, not gzipped.
bam_pileup: Improved read pair overlaps clipping. Disabled for now as more testing is needed.
Merge branch 'develop' of github.com:samtools/samtools into develop
This is a backup commit. Samtools mpileup seems to be working well in this version, but should be still considered experimental.
Merge branch 'with-htslib' of github.com:samtools/samtools into with-htslib
Added new forgotten file
bgzip: Do not overwrite input files when -b or -s are given
Moved bamcheck into "samtools stats"
Moved bamcheck into "samtools stats"
mpileup backup commit: New test annotation
Phony force target in Makefile
mpileup: Trial implementation of MWU CDF (rather than prob.)
New header file: samtools.h
mpileup: Fix in CDF version of MWU
Merge branch 'with-htslib' of github.com:samtools/samtools into with-htslib
mpileup: MWU CDF calculation in some cases returns value bigger than 1. Added a temporary check until this is resolved.
mpileup: fixed silly a typo in the previous commit
New test and updated VCF header samtools command string
MWU correction for ties
stats: Removed unused stats code (NMQ)
mpileup: Updated to the latest htslib API; disabled tie correction in MWU for now, as the results look suspicious
mpileup: Updated to htslib vcf module changes
Resolved merge conflicts
Merge branch 'develop' of github.com:samtools/samtools into develop
jsimpson (1):
constify input parameter to faidx_fetch_seq
pd3 (4):
Merge pull request #43 from peterjc/depad_bins
Merge pull request #44 from peterjc/check_bins
Merge pull request #62 from jts/develop
Create README.md
peterjc (7):
Update BIN values in 'samtools depad'
Verify old BIN value of reads during 'samtools index'.
Update 'samtools depad' help text regarding FASTA reference file
Should update POS on unmapped reads in 'samtools depad'
Slightly more detailed error message for debugging.
Show reference name in bad BIN error message
Correct BIN check for CIGAR less reads
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