- Adjust MBA read overhang clipping to be consistent with past behavior (#1571)
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- 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)