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v.0.1.22

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@GregoryFaust GregoryFaust released this 18 Jun 20:52
· 27 commits to master since this release
v.0.1.22
3fe403f

This release addresses the following issues:

  • Add -M option. Use of -M is backward compatible with the samblaster behavior since release 0.1.15 in which alignments marked with both FLAG values 0x100 and 0x800 were treated as supplemental alignments for the purposes of identifying split-reads. The new default behavior is compliant with the latest SAM specification and treats only reads flagged with 0x800 as supplemental. The -M option can (and should) be used with older alignment files created when chimeric reads were marked 0x100, or ones produced by recent versions of bwa mem using its -M option. See README.md for details.
  • Bug fixes for buffer overruns that sometimes occurred while adding the duplicate flag or mate tag information to output lines.
  • The 'N' CIGAR op is now supported, as well as multiple clip ops ('S' and/or 'H') at the beginning or end of a CIGAR string.
  • An @pg line is now placed in the header of all output SAM files.
  • SAM headers with up to 32,000 contigs may now be supported if the system being used can allocate sufficiently large arrays.
  • Add --ignoreUnmated option. This option is not recommended for general use. It disables checks in samblaster that detect incorrectly sorted or malformed input files. However, it can be useful in cases in which some alignments have been filtered out of an otherwise well formed and read-id (QNAME) grouped input file.
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