[med-svn] samtools annotated tag 0.1.20 created (now 6e3a894)

Mon Aug 18 01:39:58 UTC 2014

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plessy pushed a change to annotated tag 0.1.20
in repository samtools.

        at  6e3a894   (tag)
   tagging  48b4b70a480f9e79f623bea3ca4731ae7e511175 (commit)
  replaces  0.1.19
 tagged by  John Marshall
        on  Fri Aug 15 09:41:14 2014 +0100

- Log -----------------------------------------------------------------
Final standalone non-htslib samtools release

Brent Pedersen (1):
      use or on the -F and -f flags so that multiple flags can be specified from the command-line.

Christopher Smowton (1):
      Fix control of compression level in bam_merge_core2

Hanspeter Niederstrasser (1):
      Add generated files to .gitignore

John Marshall (18):
      Merge pull request #50 from mp15/char_array
      Merge pull request #53 from brentp/or_flags
      Add Travis CI control file
      Ensure travis's $(CC) overrides our Makefile's
      Fix thinko: a shell variable, not a make variable
      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
      Don't set text-is-cached flag if reading headers encountered EOF
      Merge pull request #20, fixmate aborts on SO:coordinate
      Fix buffer overflow
      Remove double fclose()
      Silence -Wstrict-prototypes warnings in main header files
      Merge cigar length check (PR #39)
      Set Git attributes similarly to the develop branch
      Release 0.1.20: final non-htslib standalone samtools

Martin Pollard (12):
      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[]

Petr Danecek (25):
      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?
      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

jsimpson (1):
      constify input parameter to faidx_fetch_seq

pd3 (3):
      Merge pull request #43 from peterjc/depad_bins
      Merge pull request #44 from peterjc/check_bins
      Merge pull request #62 from jts/develop

peterjc (9):
      Raise error if give @HD SO:coordinate to 'samtools fixmate'
      Catch overflow in n_cigar and give an explicit error.
      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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