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picard-tools-1.109.zip 2014-03-10 48.2 MB 0
README.txt 2014-03-10 1.8 kB 0
Totals: 2 Items   48.2 MB
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
Source: README.txt, updated 2014-03-10

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