[med-svn] [htslib] annotated tag 0.2.0-rc7 created (now ca254fe)

[Charles Plessy]

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

        at  ca254fe   (tag)
   tagging  c6f85311bd4a44f28b618dd8b73eaab79a601494 (commit)
  replaces  0.2.0-rc6
 tagged by  John Marshall
        on  Wed Mar 12 15:16:50 2014 +0000

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

James Bonfield (5):
      The default CRAM version is now 2.1. This is now the official release
      Fixed EOF check. The usual code path had the correct check, but an
      Bug fix to the SAM header padding. It could go negative and then fail
      Reduced the number of realloc calls zlib_mem_inflate(), while
      Fixed a bug when loading in fasta files consisting of all sequence on

John Marshall (14):
      Merge pull request #60, CRAM EOF block improvements
      Merge pull request #62, minor CRAM updates
      Check cram_eof() before calling cram_close()
      Keep the style of the surrounding code
      Add HTS_IDX_NONE and document HTS_IDX_*
      Merge #68, fix incorrect length given to MD5 calculation
      Add 'a' (append) mode letter; propagate mode letters
      Add "data:blahblah" in-memory hFILE backend (read-only)
      Use hFILE rather than knet in test_and_fetch()
      Merge #70, fetching of remote BAM/VCF indices
      Rewrite __skip_tag() as skip_aux()
      Add sam aux field tests
      Merge sam_format1() and __skip_tag() fixes (PR #73)
      Add ks_release() to kstring.h

Petr Danecek (12):
      vcf: Abort on broken VCFs with multiple/trailing spaces/tabs
      vcf: Don't let unpack_*_core forget the to-be-freed pointer
      hts_expand0: type ptr properly, it can be of different type
      To avoid confusion, make bcf_get_*_int and bcf_update_*_int symetric
      hts_idx_load: Print warning when index is older than data
      Make synced reader aware of bcf_hdr_set_sample(), expanded docs
      synced_reader: New bcf_sr_region_done macro
      bcf_translate: Catch unchecked errors
      More sensible Quals of matching bases in overlaps
      Ignore operation-not-supported errors in fd_flush
      vcf: Allow omitted trailing FORMAT fields
      synced_reader: Init position correctly

Rob Davies (2):
      Fixes incorrect MD5 calculation in cram_write_SAM_hdr
      Fix sam_format1 failure on lines ending in integer/float tags and issue #63

Shane McCarthy (1):
      fix remote fetching of regions for bam and vcf

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