Picard release 1.82
17 December 2012
- Speed up parsing of SAM header by precompiling regexes and by using StringUtil.split rather than String.split, and by avoiding throwing exception in non-exceptional situation in ISO-8601 date parser.
- FastqRecord.java: Allow null to be passed to any ctor arg.
- Added utility for automatic detection of quality encodings of fastqs and bams; incorporated into FastqToSam so no format need be specified; incorporated into ValidateSamFile so that an warning is generated if the BAM is not Standard/Phred-encoded
- SAMFileWriterFactory.java: Fix bug in which setting maxRecordsInRam caused an exception when creating a BAM writer.
- Refactor SAMTextReader to allow a String in SAM text format to be parsed independently by new class SAMLineParser.
- MarkDuplicates now adds PG records (chaining and uniquifying appropriately) by default. The values for all the attributes of the PG record have reasonable default values. In order to get the previous behavior of not adding PG record, pass command-line argument PROGRAM_RECORD_ID=null.