Picard release 1.51
15 August 2011
- Add support for array tag values (type B) for signed and unsigned byte, short, int; and for float. Note that previously byte arrays were stored as hex ascii string (type H). Type H will still be read, but no longer written. The only exception is that if a BAM record containing a tag of H type is read from a file, and none of the variable length part of the BAM record is changed, then if the BAM record is written to another file, the tag will still be H type.
- MergeBamAlignment.java: Fix bug triggered when EXPECTED_ORIENTATIONS is not set on the command line.
- MergeSamFiles.java: Fix bug created 7/28 in which if input were unsorted, SORT_ORDER=coordinate was ignored.
- MergeBamAlignment.java: Add option to disable soft clipping if 3' end of read extends past 5' end of mate.
- insertSizeHistogram.R: change script so that spaces are tolerated in sample/library names, columns separated on tabs only.
- SAMReadGroupRecord.java: Support FO (flow order) and KS (key sequence) attributes of read group.
- meanQualityByCycle.R, qualityScoreDistribution.R: Added tab separator for reading metrics files instead of default whitespace separator, to better handle data that includes sample names which may have spaced in them.
- BlockCompressedInputStream.java: Lazily initialize ByteArrayOutputStream so that it is not allocated if readLine is never called.
- CollectRnaSeqMetrics.java: Added check that there's actually data in the histogram to plot before calling R.