Picard release 1.64
12 March 2012
- Modified MeanQualityByCycle so that it does not try to generate an R plot if there is no data in the metrics file.
- IlluminaUtil.java: change delimitor for multiple-barcode concatenation from slash to hyphen.
Adding documentation links
* CommandLinePrograms now print web documentation link in Usage
* The FAQ link is printed when exceptions are thrown
- Fixed NPE in SAMReadGroupRecord.getRunDate().
- CollectAlignmentSummaryMetrics.java: Fix for problem where PF_ALIGNED_BASES AND PF_MISMATCH_RATE were being calculated on all aligned bases, not just PF.
- IlluminaUtil.java: Added a set of "dual indexed" adapters.
- IlluminaDataProvider and dependent classes (IlluminaBasecallsToSam, ExtractIlluminaBarcodes) will no longer load/copy files and data for skipped cycles
- IlluminaDataProvider no longer parses position files to get tile/lane information. It get's this from any available parser (and therefore avoids unnecessary parsing of position files).
- SamToFastq.java: Fix for bug whereby the FastqWriters were being close()'d multiple times if not outputting per read-group and multiple read groups were present in the input sam/bam file.