Picard release 1.62
12 Febuary 2012
- IlluminaDataProvider now supports (and prefers) BCLs and other binary data types over QSeqs. If BCLs,Pos,Locs,Clocs, or filter files are present then IlluminaDataProvider will use these file formats. However, if one type of data requested requires the use of QSeqs then QSeqs will be used for all data provided (to avoid unecessarily parsing extra files). This changes affects ExtractIlluminaBarcodes and IlluminaBasecallstoSam. READ_STRUCTURE argument is now required for both these programs.
- AbstractAlignmentMerger.java: Improve error report if no sequence dictionary found for reference fasta.
- SAMRecord.java: Avoid String.intern in set(Mate)ReferenceName if the string can be obtained from the sequence dictionary, because intern is surprisingly slow.
- SAMSequenceRecord.java: Don't use regex to truncate sequence name at first whitespace, to improve speed.
- SAMTextReader.java: Don't use regex to validate read bases, to improve speed.
- CalculateHsMetrics.java: Minor change to allow direct setting of the bait set name via a command line parameter instead of inferring it from the filename. Inference is still used if explicit name isn't passed.
- SamToFastq.java: create zero length FASTQ/SECOND_END_FASTQ files when there are zero reads per read group(s)
- DownsampleSam.java: Updated DownsampleBam to ignore all non-primary alignments so that pairs don't get mishandled.