• Simplify BedToIntervalList by not reimplementing coordinate conversion (#1292)
• Removing strange import in gradle.settings (#1291)
• Updated the documentation for SortSam to be clearer in detailing Queryname-sort tie-breaking
• Include aligned adapter reads in metrics (#1282)
• Fix "end" tag in inverted variants in liftover VCF. (#1268)
• Yf stratify chimeric (#1269)
• added comment about versioning of the tiebreaking
• catching the tool help output as well
• responding to review comment
• updated the documenation for SortSam where it was somewhat misleading