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Releases: broadinstitute/picard

2.27.0

06 Apr 21:22
@gbggrant gbggrant
2.27.0
b1e01c2
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2.27.0
  • Upgrade google-cloud-nio to match gatk (#1792)
  • Add support for documentation generation for metrics classes. (#1782)
  • Simplify handling of paths for input in BuildBamIndex.java (#1787)
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2.26.11

23 Feb 22:22
@jessicaway jessicaway
2.26.11
a03ed41
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2.26.11
  • In GtcToVcf, set infinite values to missing ('.') in the VCF. (#1777)
  • Correct logic to have ExtractBarcodesProgram properly match for all Ns (#1775)
  • Cluster Visualization Python Script (#1701)
  • Detect worker thread exception sooner, and stop other workers. (#1772)
Assets 4
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2.26.10

03 Jan 19:15
@gbggrant gbggrant
2.26.10
9379c36
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2.26.10
  • Update log4j to v2.17.1 (#1768)
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2.26.9

20 Dec 21:27
@gbggrant gbggrant
2.26.9
71213e7
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2.26.9
  • Update log4j to v2.17 (#1766)
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2.26.8

16 Dec 01:34
@gbggrant gbggrant
2.26.8
889be49
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2.26.8
  • Update Picard to Log4J 2.16.0 (#1762)
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2.26.7

14 Dec 01:32
@gbggrant gbggrant
2.26.7
cc3a779
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2.26.7
  • Upgrade Barclay. (#1760)
  • Update log4j version 2.15 to address CVE-2021-44228
  • Clarified comment for purpose of GatherVcfs (#1758)
Assets 4
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2.26.6

24 Nov 14:46
@gbggrant gbggrant
2.26.6
9880d0d
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2.26.6
  • Fix error in Picard jar packaging that prevented it from running under Java 11. Make the shadowJar multi-release. (#1749)
  • Fix picard doc on java 11 (#1750)
  • Change IlluminaBasecallToFastq to make the parameter ADAPTERS_TO_CHECK to be null by default (#1745)
    ** Note that this reverts the behavior of IlluminaBasecallsToFastq back to what it was in Picard release 2.26.0 and before.
  • Fix data provider for IlluminaBasecallsToSamTest (#1752)
Assets 4
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2.26.5

10 Nov 19:53
@gbggrant gbggrant
2.26.5
80e79fe
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2.26.5
  • Fixed bug in initialization of ExtractIlluminaBarcodes perfect score array. (#1744)
  • Removed deprecated parameter 'IS_NOVASEQ' from CollectIlluminaLaneMetrics. (#1736)
  • Updated the GKL version to 0.8.8 (#1733)
  • Added validation for existence of .bpm file to CompareGtcFiles (#1743)
Assets 4
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2.26.4

26 Oct 21:36
@gbggrant gbggrant
2.26.4
b2bf5da
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2.26.4
  • Fixed a bug in IlluminaBasecallsToFastq where ADAPTERS_TO_CHECK could not be set as a CLP argument. (#1740)
  • Fixed a bug in GtcToVcf where where SOURCE fields populated from the Illumina manifest that contain a semicolon may be incorrectly populated in the INFO field of the VCF (#1738)
  • Updated CombineGenotypingArrayVcfs to handle differences in INFO:SOURCE field of a VCF generated by GtcToVcf (#1739)
  • Added more logging to IlluminaBaseCallsToSam/Fastq (#1735)
Assets 4
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2.26.3

12 Oct 19:15
@gbggrant gbggrant
2.26.3
b5732e1
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2.26.3
  • Added CLP that can combine multiple QualityYieldMetrics files (#1717)
  • Added description of the gtcCallRate field in the VCF Header. (#1730)
  • If deprecated parameter MAX_READS_IN_RAM_PER_TILE is specified, have IlluminaBasecallsToFastq set MAX_RECORDS_IN_RAM appropriately. (#1726)
  • Minor updates: https, new urls, license year (#1723)
Assets 4
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