• Make cram valid input to remaining CLPs (#1622)
• Add on the fly demux and speed up barcode matching. (#1649)
• Cleaned up some variable names and order in the alignment metrics code. (#1707)
• Added some more skew-resistent metrics for read length (#1706)
• Fix typo in usage (#1703)
• HaplotypeMap bug fix (#1702)
• Fix bug in CollectSamErrorMetrics (#1618)