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Releases: broadinstitute/picard

2.20.1

13 May 20:25
@snovod snovod
2.20.1
a759d3c
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2.20.1
  • Enabled CRAM input into MarkDuplicates. (#1275)
  • Make CollectSamErrorMetrics show up in docs (#1326)
  • Sort CRAM test that are used with tests that create an index. (#1317)
Assets 4
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2.20.0

29 Apr 15:39
@gordonwade gordonwade
2.20.0
901ba1a
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2.20.0
  • Add fingerprint Metric (not FingerprintingMetric) (#1312)
  • liftovervcf: remove '##reference=...' and set the new one. (#1321)
Assets 4
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2.19.2

23 Apr 18:37
@gordonwade gordonwade
2.19.2
11ab5cc
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2.19.2
  • GL-143 Move the probe metrics into TargetMetrics and add a test for HsMetrics (#1318)
  • liftovervcf without sorting the variants (#1306)
Assets 4
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2.19.1

18 Apr 13:55
@mreinema mreinema
2.19.1
5843068
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2.19.1
  • Fix CollectInsertSizeMetrics temporary file creation. (#1313)
  • update google cloud NIO provider (#1300)
  • GL-143 remove fields defined in base class (#1307)
  • Add ability to crosscheck (and check) fingerprints on CRAMS directly. (#1302)
  • Fixes assert statement in UmiAwareMDWMC tester (#1271)
  • Update README.md (#1293)
  • Factor out a SamComparison class from CompareSAMs for reuse. (#913)
  • Update CreateSequenceDictionary.java (#1286)
  • fix a typo (#1296)
Assets 4
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2.19.0

25 Mar 21:02
@jacarey jacarey
2.19.0
ba9b355
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2.19.0
  • Updating htsjdk to 2.19.0 (#1297)
  • Add COUNT_OUTPUT input parameter to IntervalListTools to output count of bases/intervals to file
Assets 4
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2.18.29

19 Mar 13:25
@sahakiann sahakiann
2.18.29
1531278
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2.18.29
  • Simplify BedToIntervalList by not reimplementing coordinate conversion (#1292)
  • Removing strange import in gradle.settings (#1291)
  • Updated the documentation for SortSam to be clearer in detailing Queryname-sort tie-breaking
  • Include aligned adapter reads in metrics (#1282)
  • Fix "end" tag in inverted variants in liftover VCF. (#1268)
  • Yf stratify chimeric (#1269)
  • added comment about versioning of the tiebreaking
  • catching the tool help output as well
  • responding to review comment
  • updated the documenation for SortSam where it was somewhat misleading
Assets 4
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2.18.27

25 Feb 16:53
@nikellepetrillo nikellepetrillo
2.18.27
21ad30b
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2.18.27
  • IlluminaBaseCallsToSam - demultiplex only when read structure has barcodes (#1281)
Assets 4
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2.18.26

05 Feb 13:23
@nikellepetrillo nikellepetrillo
2.18.26
42c8ee0
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2.18.26

Added handling for indels within CollectHsMetrics and CollectTargetedPcrMetrics. (#1273)

Assets 4
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2.18.25

23 Jan 14:06
@mreinema mreinema
2.18.25
6ad57dc
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2.18.25
  • Update our jdk base image (#1270)
Assets 4
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2.18.24

22 Jan 16:07
@mreinema mreinema
2.18.24
b15d007
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2.18.24
  • update to htsjdk 2.18.2 (#1267)
  • changing ADD_PG_TAG_TO_READ to boolean (#1262)
  • Liftover all indels in flipped strand (#1266)
  • fixing a subtle bug with keeperOrNull
  • Histogram of duplicate set sizes to be reported in the MarkDuplicates metrics file (#569)
  • Tool to add OA sam tag to reads (#1202)
  • optimization A
  • Changed the OpticalDuplicateFinder to no longer be order dependant in its output.
Assets 4
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