Picard release 1.96
29 July 2013
- Support for the 0x800 supplementary alignment flag within Picard. Tools which previously only processed primary and ignored secondary alignments will now ignore secondary and supplementary. MergeBamAlignment will pass supplementary alignments along in the output BAM.
- Various changes have been made so that Picard programs and libraries will work properly with Java 7. However, Picard will continue to be compiled with Java 6.
- Added funcitonality to .bcl-reading command line programs (IlluminaBasecallsToSam, IlluminaBasecallsToFastq, and ExtractIlluminaBarcodes) to better handle qualities less than 2 via BclQualityEvaluationStrategy. When an application encounters such a quality score, it used to throw an exception immediately; now, it will convert write a quality 1 to the underlying file (bam, fastq, etc.), and at the end of reading the BCLs, it may or may not throw an exception depending on the strictness of the BclQualityEvaluationStrategy. It will always log a warning message if a quality is encountered, regardless of whether or not an exception is thrown. By default the minimum acceptable quality score is still 2, but it may be controlled via the command-line option MINIMUM_QUALITY.
- Performance improvements for VCF I/O.
- Deprecated AsciiLineReader; instead, use LineReaderUtil.fromBufferedStream().
- Added new BufferedReader-like class, LongLineBufferedReader, with performance improvements for longer-lined files.
- Added an asynchronous line reader, AsynchronousLineReader, which offloads the work of parsing lines into another thread.
- Configure Picard-public so that (1) IntelliJ and ant compile to different places and (2) IntelliJ ignores all of the ant compile locations (so that, for example, it does see all the ant .class files and think they are part of the source). This should prevent ant builds from having an effect on how IntelliJ operates.