Picard release 1.74
30 July 2012
- Added a new "ProgressLogger" class that facilitates more useful and standard progress logging for any program that iterates through a stream of SAMRecords. Adapted most command line programs to use it.
- Add support for targetedPcrMetrics and collected common HsMetrics and TargetedPcrMetrics behavior into TargetMetricsCollector
- New program CollectTargetedPcrMetrics
- MultiHitAlignedReadIterator.java: Handle case where an alignment record has no cigar elements that consume both the read and the reference (e.g. the read is all soft-clipped)