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Commits on Jan 24, 2020

• Add files via upload

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  haodongchen

  authored
  79647d2

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Commits on Jan 13, 2020

• Fix a bug to allow setting the primary flag on SamRecord (#562)

  

  clintval

  authored and

  nh13

  committed
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Commits on Jan 9, 2020

• Add the `primary` keyword for accessing a SamRecord's secondary flag (#560)

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  rnazad

  authored and

  nh13

  committed
  dfb8713

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Commits on Dec 10, 2019

• Add in another date format Illumina uses in the RunInfo.xml

  tfenne

  committed
  e7ac607

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Commits on Nov 7, 2019

• Updated version to 1.2.0-SNAPSHOT

  tfenne

  committed
  11a4b9e

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• Bump version for release. Push htsjdk to non-SNAPSHOT release.

  tfenne

  committed
  92a8ad4

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• Enabling consensus read generation from SE data. (#550)

  tfenne

  authored
  3a4f099

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Commits on Nov 6, 2019

• Add a few more methods on ProgressLogger (#512)

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  nh13

  authored
  3ffb374

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• Bug fix: output consensus UMI bases (RX) was wrongly computed (#489)

  nh13

  authored
  fdeac40

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• Do not close the given stream when building a FastqSource (#545)

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  nh13

  authored
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• Add options for the RX/MI tags to CollectDuplexSeqMetrics (#548)

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  nh13

  authored
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Commits on Oct 24, 2019

• Add classes for reading and writing interval lists (#535)

  nh13

  authored
  dc187f7

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• Fix to not throw an exception if the machine's hostname cannot be determined. (#544)

  

  tfenne

  authored and

  nh13

  committed
  36c460a

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Commits on Oct 10, 2019

• Emit the currently-in-use inflater/deflater on tool startup (#537)

  

  clintval

  authored and

  nh13

  committed
  2100905

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Commits on Oct 7, 2019

• Do not use the Intel inflater or deflater on OS X 10.14 (#534)

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  nh13

  authored
  8f9d01a

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Commits on Sep 24, 2019

• Count homopolymers and calculate gc content (#533)

  

  mjhipp

  authored and

  nh13

  committed
  4f11a43

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Commits on Aug 29, 2019

• Added method to Sequences object to given IUPAC code for any combinat… (#525)

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  tfenne

  authored
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Commits on Aug 28, 2019

• Fix to ensure that filters are converted in a reliable fashion when reading VCFs.

  tfenne

  committed
  f59fc28

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• Minor changes to ReferenceSetBuilder to allow for fuller dictionaries.

  tfenne

  committed
  225c29e

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Commits on Aug 20, 2019

• Same fix, in RandomizeBam, that was applied for RandomQuery sorting to prevent collisions.

  tfenne

  committed
  47d7f41

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Commits on Aug 19, 2019

• Don't try to index BAM files that can't be indexed with HTSJDK. (#520)

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  tfenne

  authored
  73d054d

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• Update SamBuilder.scala (#513)

  nh13

  authored
  8dc50dd

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• Improve DemuxFastqs documentation (#519)

  nh13

  authored
  3cb4d4d

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Commits on Aug 18, 2019

• Use LnErrorRatePostLabeling in the consensus caller. (#496)

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  nh13

  authored
  9c49e97

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• Add option to set sampleName in SamBuilder (#514)

  

  mjhipp

  authored and

  nh13

  committed
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Commits on Aug 16, 2019

• Fix hash collision problem in SamOrder.RandomQuery.

  tfenne

  committed
  3b8f94c

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Commits on Aug 12, 2019

• Add the clear() method to SamBuilder. (#515)

  nh13

  authored
  0731fce

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Commits on Aug 6, 2019

• More minor fixes to README.

  tfenne

  committed
  8f9a006

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• Updating version to 1.1.0-SNAPSHOT and fixing some versions in the docs.

  tfenne

  committed
  ee7dcbd

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• Prep for the 1.0.0 release.

  tfenne

  committed
  674a41e

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Commits on Aug 5, 2019

• Fix for reading/writing VCFs that have no-call alleles in the genotypes.

  tfenne

  committed
  431ca7a

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Commits on Aug 1, 2019

• Scala VCF API (#501)

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  tfenne

  authored
  17cc57a

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Commits on Jul 30, 2019

• Removed some long-standing deprecations in ClipBam and DemuxFastqs.

  tfenne

  committed
  6cba5d5

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• Moved to cross-building 2.12 & 2.13, dropping support for 2.11.

  tfenne

  committed
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Commits on Jul 24, 2019

• Speeding up CallDuplexConsensusReads.

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  nh13

  committed
  426a258

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