Picard Release 1.53
26 September 2011
- ReorderSam.java: Get mate reference index before changing header on SAMRecord, in case input is SAM format and reference index is found by looking up reference name in header.
- SAMSequenceDictionary.java: Added getReferenceLength method to sum the lengths of the sequences in the dictionary.
- SAMRecord.java: Add notes about lack of validation when values are set into SAMRecord.
- Add mechanism for converting a SAMRecord to SAM-text format, without having to write a SAM file. Patch courtesy of Fred Long.
- CollectRnaSeqMetrics.java: If rRNA.interval_list has not been provided, write empty values for RIBOSOMAL_BASES and PCT_RIBISOMAL_BASES rather than 0.
- IlluminaBasecallsToSamConverter.java: Small change to output the "BC" tag with the barcode read sequence, but into the unmatched read file only.
- Add Bzip2 support to Picard.
- CollectAlignmentSummaryMetrics.java: modified chimerism % calculation so that the denominator is only those reads considered as possible chimeras (was all hq pf reads)
- EstimateLibraryComplexity.java: Fix bug in which, if read names were not standard Illumina syntax, all dupes were considered to be optical dupes, and thus library complexity could not be estimated.
- IlluminaBasecallsToSam refactor: Removed support for Bustard 1.1.
- EstimateLibraryComplexity.java: Initialize PairedReadSequence.readGroup to -1 so that no read group is detectable. Fixes ArrayIndexException.