[Samtools-announce] Picard release 1.109

[Alec W. <al...@br...>]

Picard release 1.109
10 March 2014

- Add buffering for BAM file writing.  By default this will be 128K.  Buffer size can be controlled via -Dsamjdk.buffer_size=<value>.  Buffer size can be controlled programmatically via SAMFileWriterFactory.setBufferSize() method.

- Added MateCigar to SAMRecord as an optional Attribute ("MC")
  - Given a SAMRecord that is part of a pair, the MateCigar attribute (MC) will contain the cigar string for that read's mate iff the mate is mapped.
  - Added getters (for String and Cigar) to SAMRecord.
  - Moved utility methods (getClippedAlignmentStart/End...) to SAMRecord and commonified with similar methods for the Read itself.
  - Added validations to MateCigar (not present when inappropriate, matches the Mate's Cigar String).

- Added the command line tool RevertOriginalBaseQualitiesAndAddMateCigar
  - meant to update a SAM/BAM to include the new Mate Cigar ("MC") optional tag.
  - additionally, allows the user to optionally revert the original base qualities ("OQ" optional tag).
  - will exit early with an INFO message if the SAM/BAM already has the "MC" tag, and therefore would not need to be reverted.

- MergeBamAlignment, CleanSam, RevertOriginalBaseQualitiesAndAddMateCigar: Make sure that the mate CIGAR (MC) does not hang off the end of the reference.  If it does, clip it, the same way we do with the record's CIGAR.

- SortSam, MergeBamAlignment: Adding logging to record progress while writing SAM records to disk when sorting.

- AbstractAsyncWriter.java: Handle case in which exception in writer thread is not detected because queuing thread is already blocking on full queue before exception occurs.

- SAMHeaderRecordComparator.java: Adding a checksum generation method for SAM RG records

-Alec