[med-svn] samtools annotated tag 0.2.0-rc9 created (now c377045)

[Charles Plessy]

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plessy pushed a change to annotated tag 0.2.0-rc9
in repository samtools.

        at  c377045   (tag)
   tagging  ddbd14b35e4531558975111ca98a9db1c1360084 (commit)
  replaces  0.2.0-rc8
 tagged by  John Marshall
        on  Fri Jun 13 14:56:06 2014 +0100

- Log -----------------------------------------------------------------
Test release RC9

James Bonfield (3):
      Ruthlessly tidied up the examples directory.
      Call hts_set_fai_filename on the output fd too so that -T has a chance
      Updated test harness to cope with CRAM now including MD and NM tags in

John Marshall (35):
      Create a print_usage() function for usage printing
      Reformat usage to (mostly) fit in 80 columns
      Minor rewording of usage to fit in 80 columns
      Fix long option has_arg inconsistencies
      Also clean test/test.o
      Use getopt.h's descriptive constants in long options array
      Use getopt.h's descriptive constants in long options array
      Reformat usage for 80 columns
      To free unaccounted_header_name, it must have been malloced
      Make merge_usage()'s parameter directly understandable
      Merge merge input and doc fixes, test stdout/stderr fixes (PRs #188, #202)
      Close orig_stderr *after* printing final error message
      Merge test harness memory leaks (PR #200)
      Fix calloc() type mismatch
      Prevent segfault when input file could not be opened
      Prevent segfault when input file could not be opened
      Test case fixed by htslib change
      Miscellaneous code tweaks
      Check for Usage output on stdout (ok) or stderr (expected failure)
      Merge bam2fq improvements and documentation (PR #204)
      Remove mpileup -M option, which has never been implemented
      Remove razip source code and remaining vestiges
      Tweak `samtools view` documentation formatting
      Merge view documentation updates (PR #218)
      Revert to ex1.sam.gz; fix mpileup command lines
      Merge examples/ tidy up (PR #226)
      Add lowercase synonyms for --VCF etc long options
      Add seq_cache_populate.pl (PR #224), add it to "make install"
      Update bam_index.o header dependencies
      Merge idxstats htslibification (PR #191)
      Merge QS-vs-PL branch into develop
      Add samtools index options to select BAI or CSI
      Add output mode parameter to bam_merge_core2 and bam_sort_core_ext
      Overhaul samtools sort options and invocation
      Merge mpileup long options (PR #205)

Joshua Randall (4):
      Fixes `samtools sort` output to always be BAM
      Removes '(forces -S)' from samtools view -T|t usage
      Updates documentation for `samtools view`
      Improves performance of `samtools merge` (slightly)

Martin O. Pollard (5):
      Reenable idxstats and convert to htslib
      Add code to separate out stdout and stderr in testing
      Make merge take union of commandline and -b inputs and test merge code
      Merge branch 'patch-1' of https://github.com/SamStudio8/samtools into merge_unioninput
      Migrate ideas from bam2fq from htslib and document

Petr Danecek (8):
      mpileup: Long options
      mpileup: support for BAM_CHARD_CLIP cigar
      stats: Simplified usage of --GC-depth, reflen not required
      stats: Check for zero-length cigars (e.g. 0D)
      mpileup: Per-sample rather than cumulative QS. (experimental)
      mpileup: Updated tests
      Merge branch 'develop' into QS-vs-PL
      mpileup: Reflect change in bcf_hdr_add_sample() usage

Rob Davies (2):
      Add seq_cache_populate.pl
      Add tests for making CRAM files using samtools view -t/-T

Sam Nicholls (17):
      Add -b parameter to samtools merge manpage
      Update samtools.1
      Match style for FILE option
      Alternate syntax for samtools merge.
      Alternate syntax for samtools merge in stderr message
      Clarify list is not a literal
      Match samtools merge manpage and stderr syntax
      Fix getline memory leak in test_bam_translate
      Fix memory leak in test_rtrans_build
      Fix memory leak in test_trans_tbl_init
      Add missing fclose of orig_stderr to test_bam_translate
      Fix getline memory leak in test_filter_header_rg
      Fix getline missing fcloses in test_parse_args
      Add missing frees to test_parse_args
      Free char* in parsed_opts in test_parse_args
      No need to set len=0 before getline
      Free all allocated names from count_RG

Shane McCarthy (2):
      Deprecate `-S`, `-D`, `-V` in favour of `-t DP,DV,SP`
      some progress for mpileup documentation

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