• ExtractIlluminaBarcodes throws a NullPointerException in the case of an empty lane directory (#948)
• Adds usage statement to UmiAwareMarkDuplicatesWithMateCigar that it shouldn't be used with RNAseq or other technologies with long gaps. (#959)
• Converted the tests of @DataProviders to using....a @dataProvider! (#941)
• Make column names in ExtractIlluminaBarcodes public, and use them in the help description (#957)
• Fixed H4 tags in README (#954)
• Extending CrossCheckFingerprint to do a serial check. (#949)
• Backport VcfToIntervalList INCLUDE_FILTERED argument from GATK. (#875)