[med-svn] samtools annotated tag 0.2.0-rc7 created (now 495a124)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.2.0-rc7
in repository samtools.

        at  495a124   (tag)
   tagging  7a871697ba5a5ab4e724f8b2a287c5beca62a52e (commit)
  replaces  0.2.0-rc6
 tagged by  John Marshall
        on  Wed Mar 12 15:16:50 2014 +0000

- Log -----------------------------------------------------------------
Test release RC7

John Marshall (18):
      Use htslib facilities instead of bam_parse_region()
      Revert unnecessary changes on tview branch
      Use sam_itr_*()/etc and enable compiling with current htslib
      Fix tview-related dependencies
      Merge pull request #93, convert tview to htslib API
      Use sam_itr_*()/etc, enabling tview on CRAM files
      Fix "Usage: ..." message
      Merge #148, links to 'sister' projects (but omitting ourself)
      Update dependencies and define _GNU_SOURCE only for bam_sort.o
      Use htslib facilities instead of bam_parse_region() etc
      Make I/O redirection portable (to Linux)
      Add test/merge/* test programs to main Makefile
      Merge pull request #70, merge improvements
      Create xfreopen() utility instead of duplicating code
      Use kstring instead of asprintf()
      Merge asprintf()->kstring rewrite and warning fixes (#161)
      Fix buffer overflow
      Use kstring instead of strndup()

Martin Pollard (64):
      Add some more comments to tview
      Reenable tview and port to htslib
      Restore sample selection to tview and add a unit test for the code doing it.
      Add a few comments to bam merging function
      WIP on header merging
      Add target id translation code and write pseudo code for building RG and PG translation tables
      Convert PG and RG pseudo code to working code.
      Further work on bam merge to fix header produced
      Fix bugs picked up by unit testing.
      More work on merging @RG and @PG tags into header.
      Unit tests for merge
      add skeleton code for PP processing
      NULLify some freed pointers.
      Unit test trans_tbl_init add test 5 for PG tags
      Fix memory leaks and finalise @PG PP handling
      Test @PG merging and PP handling
      Integrate new header merging code into bam_sort main function
      Clean up old dead code
      Fix case where PG or RG tag is present on read but not in header.
      Add test bams
      Fix spaces to tabs
      Eliminate compiler warnings in a cross-platform safe way.
      Add unit test for bam_translate (WIP)
      Fix edge case
      Add unit test for tid translation
      Add additional unit tests for bam_translate for PG and RG tags.
      Adjust how merge handles duplicated PG and RG tags.
      Add command line support for combining tags
      Don't merge header into itself
      Correct header length in test
      Fix memory leak in trans_tbl_init
      Enhance description of what we do
      Add warning when merging causes coordinate sort to be lost
      Reorder merge code so that BAM gets translated before it is inserted into heap.
      Create slightly more sophisticated unit tests for merge
      Convert merge reverse translation build to own function.
      Ensure make only runs on make test
      Add clock based randomness to merge and option to fix random seed.
      Correct lost sort order detection in merge
      Fix regex to pick out sequence ids
      Add rtrans_build unit test stub
      More work on rtrans_build unit test.
      Fix position of bam_translate in merge read loop.
      Deal with case where merged region does not exist in header of one of our input files.
      hts_iter_t is not a pointer unlike it's predecessor
      Add function to prettify header output by sorting it by defined order.
      Instead of relying on NULL iter in merge use HTS_IDX_START
      Ignore generated test files
      In bam sort and merge change:
      Fix merge unit tests under Linux
      Initialise un-inited variable in test_bam_translate.
      Revise merge header matching regex from spec
      Make it easier to tell merge test phases apart
      Apparently some programs put spaces into their @PG and @RG ID's.
      Add option to vary level of verbosity.
      Fix bug where wrong flag was being checked in header merge (merge rg vs merge pg)
      Add PG tags to @RG lines testcases.
      When merging instead of segfaulting when there is no index, return an error.  Need to think of better ways to handle this.
      Fix to use htslib commands.
      Port bam_sort.c completely to new API.
      Fix up tests for htslib architecture
      Add -b option to merge to allow the specification of a list of files as alternative to putting them on the command line.
      bam_merge: get rid of asprintf warnings
      bam_merge tests: fix warnings

Mike Lin (1):
      Fix control of compression level in bam_merge_core. The setting was ineffective due to a minor copy/paste error.

Petr Danecek (5):
      mpileup: Fixed broken IMF annotation
      Added mpileup tests for CRAM
      Make int size explicit for bcf_get_*_int calls
      stats: More understandable output fields naming
      Updated mpileup test to reflect change in overlap quals

Rob Davies (1):
      Limits -Q option (qual_scale) to sensible range 0 to 93.

dbolser-ebi (1):
      Added links to 'sister' projects.

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