• Adds support for reading CSI indexes. (#998)
• Fix default PAR values for hg37 for FindMendelianViolations (#1600)
• using guava instead of rolling my own CollectionsUtils... (#1619)
• Added a metric to CollectAlignmentSummaryMetrics for the mean length of 3' softclips (#1586)
• Add functionality to not combine abutting intervals (#1608)