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)

2.23.1

• -cleanup and better error messaging (#1529)

2.23.0

• Added GtcCallRate to GtcToVcf, parse it out and report it in CollectArraysVariantCallingMetrics. (#1525)
• Bugfix for IdentifyContamiant + small improvements to Fingerprinting (#1496)
• GtcFile now uses bpm rather than bpm.csv (#1517)

2.22.9

• gl-916 add pipeline version to metrics (#1515)
• Update htsjdk to 2.22.0 (#1518)

2.22.8

• Fixes edge case where soft-cliped portion of a read ends up at a nega… (#1513)
• GatherVcfs and MergeVcfs: add COMMENT= + GatherVcfs SORT (#1480)

2.22.7

• Change default in RevertSam for restoring hard-clips to true (#1509)
• NP-remove_r_from_argument (#1508)
• Fix for corrupted CO tag issue (#1461)

2.22.6

• Hardclip adapter option in MergeBamAlignments (#1484)

2.22.5

• fix CollectSequencingArtifactMetrics so that it doesn't die when encountering IUPAC bases (#1506)

2.22.4

• GL-970. (#1497) - Have CompareMetrics consider two NaN metrics equal. Added absolute difference.