[Samtools-announce] Picard Release 1.31

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

Picard release 1.31
20 Sep 2010

- BAM index generation: This release contains code to generate BAM indices, both for existing BAM files, and also to generate a BAM index automatically in conjunction with the writing of a BAM file.  This is beta quality code.  We encourage people to try it out and report any problems, but we do not consider it to be production quality at this point.

- FixMateInformation.java: Refactored to permit easier extension by sub-classes

- CollectInsertSizeMetrics.java: Fixed to no longer throw an exception if there is insufficient data to plot.  Also added an optimization to stop when it reaches the unmapped reads at the end of the file.

- When writing BAM and configured to automatically generate bai or md5, do not try to write .bai or .bam.md5 if file is not a normal file.

- SAMSequenceRecord.java: Treat sequence length of 0 as unknown length, and do not return false from isSameSequence because one of the sequences has this length and the other has something different.

- HsMetricsCalculator.java: Minor edit to how bait set name is derived from the bait intervals file.

- CollectAlignmentSummaryMetrics.java: Allow adding/overriding of ADAPTER_SEQUENCE option.

- CommandLineParser.java: Command line written to stderr did not show the correct values for lists, despite internally the value being correct.



-Alec