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Releases: broadinstitute/picard

2.25.0

10 Feb 19:17
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  • Update htsjdk 2.23.0 -> 2.24.0 (#1641)
  • Include common (engine-level) args in help output. (#1580)
  • [refactor] Large refactor of IlluminaBaseCallsConverter (#1626)
    • Refactor the IlluminaBasecallsConverter and IlluminaDataFactory to normalize creation when dealing with cbcls vs bcls
    • Include a BasecallsConverter that doesn't do read name sorting by default
    • Performance enhancements

2.24.2

03 Feb 16:13
4a9c42d
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  • Added mapping quality concordance functionality to CompareSAMs (#1617)
  • Yf fix il to bed sorting (#1612)

2.24.1

21 Jan 20:29
74a85ab
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  • adding read information to an error. (#1621)

2.24.0

04 Jan 16:46
e976c2a
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  • 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

08 Dec 20:36
028ecc2
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  • 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

14 Oct 18:10
4c937e5
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    • 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

13 Oct 14:10
bf70347
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  • 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

30 Sep 19:50
c631f56
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  • Remove deprecated syntax (#1585)
  • Fixed a bug in MergeBamAlignment (#1581)
  • Support standard input in IntervalListTools (#1582)

2.23.5

29 Sep 14:57
18fc8bb
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  • Add testing for methods within sex enum (#1578)

2.23.4

03 Sep 17:47
571ec3a
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  • 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)