Picard release 1.75
13 August 2012
- Added method to make a read unmapped and a method to check whether any cigar element consumes both read and reference bases to SAMUtils; used these methods in AbstractAlignment merger to catch reads with cigar strings that don't consume any read or reference bases (e.g. all soft-clipped) and make them unmapped
- Augmented plots for GC Bias Metrics, Mean Quality by Cycle, Quality Score Distribution, and RNA Sequence Coverage. Specifically, if the plot was generated from a read group .bam, the title of the plot includes the read group's library.
- IlluminaDataProvider.java: Produce more useful error output by printing out the class of the parser that's failing
- Support SeekableStream BAM index.
- build.xml: Added single-jar packaging target tasks. Consolidated package-commands task.