2.24.1

• adding read information to an error. (#1621)

2.24.0

• 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)

2.23.9

• Fast fail if R is not installed in tools that use R (#1613)
• • enable CollectIndependentReplicateMetrics to read a cram file (#1599)
• Remove cluster intensity data.
• Check Sequence Dictionaries Match in CollectWgsMetrics (#1610)
• Add flowcell location stratifier for CollectSamErrorMetrics (#1603)
• GtcToVcf should not fail if AS tag is missing (#1445)
• Increase fraction of target coverage for panel metrics (#1542)

2.23.8

• • There was a buggy interactino between CollectMultipleMetrics and CollectAlignmentSummaryMetrics with regards to the collection and emission of the readlength histrogram. This PR fixes it. (#1595)

2.23.7

• extra protection and messaging for the histogram of read lengths in CollectAlignmentSummaryMetrics (#1593)
• Safely run DownsampleSam multiple times (#1584)
• MBA deletion edge case alternate solution and minor bug fix (#1589)

2.23.6

• Remove deprecated syntax (#1585)
• Fixed a bug in MergeBamAlignment (#1581)
• Support standard input in IntervalListTools (#1582)

2.23.5

• Add testing for methods within sex enum (#1578)

2.23.4

• Adjust MBA read overhang clipping to be consistent with past behavior (#1571)
• • add support for CRAM reading in IdentifyContaminant and ExtractFingerprint (#1572)
• Yf fix typo in histogram column name asm (#1568)
• Use new IntervalMergingIterator to merge intervals on the fly (#1456)
• Several changes to metrics collections (AlignmentSummaryMetrics and WgsMetrics) + some fluff (#1555)
• Make Fingerprint checking fail when run on a truly unsorted file (currently it returns a non-informative fingerprint) (#1556)
• Added a simple test for LiftoverHaplotypeMap (#1550)

2.23.3

• Add haplotype map liftover (#1457)
• Determine arg parser to use. (#1265)
• Update CREATE_INDEX arg javadoc. (#1547)
• Update README.md (#1543)
• Use a mutable list when initializing MergeBamAlignment MATCHING_DICTIONARY_TAGS arg. (#1545)
• New CheckDuplicateMarking CLP (#1507)

2.23.2

• Update to htsjdk 2.23.0 (#1537)
• Upgrade to Barclay 3.0.0. (#1526)