- Converted VariantCallingMetrics to using MergableMetricsBase (#552)
- fix Exception thrown in MergeBamAlignment when NM tag was present (#744)
- add IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS); to MergeVcfs (#729)
- Tests for CollectOxoGMetrics, CollectJumpingLibraryMetrics and BamTBfq classes
- Adding metrics for estimating strand specificity. (#733)