[med-svn] [htslib] annotated tag 0.2.0-rc9 created (now 063bee7)

[Charles Plessy]

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

        at  063bee7   (tag)
   tagging  6a5b9fd660b4d09541bc413329e5aafeb84346b0 (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 (5):
      Changed the initial CRAM EOF value to be 1 (expected EOF) and then
      Sanitised the setting of fd->empty_container into one place. This also
      Removed bogus "Unable to find ref name"* errors when converting a SAM
      sam_hdr_write() now calls cram_load_reference if
      Set NM/MD creation to be on by default.

John Marshall (10):
      Fix forgotten s/razip/bgzip/
      Remove RAZF source code
      Check CIGAR string has fewer than 2^16 operators
      Fix "unrecognized CIGAR operator" diagnostic
      Return 0/-1 rather than bool; parenthesise C macro
      Merge API functions for index statistics (PR #83)
      Check index file magic numbers and I/O
      Fix endianness problems outwith CRAM code
      Add sam_open_mode() API function
      Remove val_unused -- use HTS_UNUSED instead

Joshua Randall (1):
      Add a comment to deobfuscate bam_cigar_type

Martin O. Pollard (2):
      Add functions for idxstats
      Improve hts_idx_get_stat to work for more file types

Petr Danecek (11):
      bgzf: Support for reading gzip-compressed files.
      Minor comment change
      bgzf: Support for FCOMMENT gzip header
      bgzf: Support the remaining optional GZIP header fields
      bcf_sr: New missed_reg_handler and bcf_sr_regions_flush() function
      vcf: New bcf_dup() function
      idx: Don't create broken .tbi or .csi when file unsorted (VCF/BCF/BAM)
      synced_reader: Removed unused code
      vcf: Change of bcf_hdr_add_sample() usage.
      bcf_write: Error message instead of assert + propagate the error up
      vcf_parse: Detect incorrect number of columns

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