Picard release 1.63
27 February 2012
- CollectGcBiasMetrics.java: Make coordinate-sort requirement explicit.
- SamPairUtil.java: Fix off-by-one error in computation of insert size; and then: Fixi a off-by-two bug introduced recently in calculation of insert size when read 1 has a higher mapped coordinate than read 2.
- SequenceUtil.java: added areSequenceDictionariesEqual()
- Implemented a tiny custom sublcass of GZIPOutputStream so that the compression level could be adjusted from the default compression level (5), and made it to that IoUtil.openFileForWriting() and friends that vector to our GZIP writing code override the default using Defaults.COMPRESSION_LEVEL which is settable via system property.
- Added a new Defaults.BUFFER_SIZE settable from system property samjdk.buffer_size that replaces IOUtil.DEFAULT_BUFFER_SIZE. Default is still 128k.
- Small performance tweak to how we identify adapter dimer in CollectAlignmentSummaryMetrics.
- ExtractIlluminaBarcodes has been modified to support multi-threaded operation.
- Add OutputFilePrefix option to BamToBfq and RunMaq