Picard release 1.54
11 October 2011
- Modify CollectRnaSeqMetrics.java to support multi-level metrics collection
- CollectAlignmentSummaryMetrics.java: Guard against PCT_CHIMERAS denominator being 0
- Refactoring of IlluminaBaseCallsToSam
- Remove upper limit on BAM record size.
- CollectAlignmentSummaryMetrics.java: Added a bunch of IF statements to protect against divide by zeros.
- Add bzip2 classes into picard jar.
- Support IUPAC ambiguity codes in SAM and BAM.
- Remove validation that requires that there be no CIGAR for unmapped read, because use of SAM for assembly has reads marked as unmapped that have CIGAR.