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Commits on Aug 25, 2016

• added function to extract SA tag and return a list of supplementary alignments (samtools#685)

  

  lindenb

  authored and

  lbergelson

  committed
  c3d5a88
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Commits on Aug 24, 2016

• Removed unused .bcf test files. (samtools#691)

  

  cmnbroad

  authored and

  lbergelson

  committed
  275cfe0
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Commits on Aug 23, 2016

• Merge pull request samtools#671 from cmnbroad/cn_validate_cram_md5

  cmnbroad

  authored
  a31f6c8
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• Throw on unrecognized CRAM encoding tag. (samtools#593)

  

  cmnbroad

  authored and

  lbergelson

  committed
  0d0da87
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Commits on Aug 19, 2016

• Remove unreferenced test files. (samtools#687)

  

  cmnbroad

  authored and

  lbergelson

  committed
  b81d036
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• Added a "RANDOM" duplicate scoring strategy. (samtools#688)

  tfenne

  authored
  0e17e07
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Commits on Aug 18, 2016

• Normalize CRAM reference bases and throw on MD5 validation failure.

  cmnbroad

  committed
  a781afa
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Commits on Aug 10, 2016

• Fix samtools#653 (samtools#672)

  

  magicDGS

  authored and

  Yossi Farjoun

  committed
  c8202f2
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• FeatureCodec.getTabixFormat() to encapsulate tabix formatting (samtools#669)

  

  magicDGS

  authored and

  Yossi Farjoun

  committed
  fba4637
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Commits on Aug 9, 2016

• Merge pull request samtools#646 from Lenbok/async_self_suppression

  droazen

  authored
  8ef565a
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Commits on Aug 3, 2016

• Merge pull request samtools#676 from samtools/dr_readme_testsingle

  lbergelson

  authored
  fa12f1f
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• Add mention of test.single to README

  droazen

  authored
  c872049
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• updating urls in tests to point to new locations (samtools#675)

  lbergelson

  authored
  38713af
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Commits on Aug 2, 2016

• Merge pull request samtools#667 from samtools/kb_AddPairedIntervalFilter

  kbergin

  authored
  b861abc
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• Expose the set of tags to reverse and reverse complement as parameters. (samtools#673)

  tfenne

  authored
  ec2d3f9
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Commits on Aug 1, 2016

• Starting

  kbergin

  committed
  702e77f
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Commits on Jul 29, 2016

• Improved SRA tests, corrected error message (samtools#638)

  

  a-nikitiuk

  authored and

  Yossi Farjoun

  committed
  0875b62
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• Fix self-suppression problem with exception handling in AbstractAsyncWriter

  Lenbok

  committed
  ea80585
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Commits on Jul 26, 2016

• Merge pull request samtools#663 from bbimber/GenotypeAttributes

  ldgauthier

  authored
  87b1e87
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Commits on Jul 25, 2016

• support genotype filters in Genotype.getAnyAttribute() and hasAnyAttribute

  bbimber

  committed
  6141de3
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Commits on Jul 13, 2016

• Merge pull request samtools#581 from magicDGS/dgs_genotypebuilder_fix

  droazen

  authored
  fcfad25
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• Added makeWithShallowCopy to GenotypeBuilder

  magicDGS

  committed
  2cc88ac
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Commits on Jul 11, 2016

• Merge pull request samtools#659 from SHuang-Broad/sh_add_unitest_for_VCFStandardHeaderLines

  nh13

  authored
  e7c7bf6
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• added unit tests, tiny clean up for VCFStandardHeaderLines

  SHuang-Broad

  committed
  9ceb00f
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Commits on Jul 7, 2016

• Merge pull request samtools#654 from SHuang-Broad/sh_GATK3_issue_1413

  lbergelson

  authored
  ee05a20
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Commits on Jul 6, 2016

• Merge pull request samtools#616 from samtools/nh_locus_info_size

  nh13

  authored
  2cb67cb
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• Add a size method to SamLocusIterator.LocusInfo.

  nh13

  committed
  fa519a3
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Commits on Jun 30, 2016

• Number tag in header line for GENOTYPE_FILTER

  SHuang-Broad

  authored
  6edf1a2
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Commits on Jun 28, 2016

• Fixed bug where SamPairUtil.setMateInfo() would omit the MQ tag if one read was mapped and the other unmapped. (samtools#647)

  tfenne

  authored
  d683012
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• made LazyInitializer a @FunctionalIterface to enable java8 sugar. (samtools#652)

  

  Yossi Farjoun

  authored
  7084c88
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Commits on Jun 25, 2016

• Allow unzipping using an offset into the uncompressed and compressed arrays. (samtools#651)

  

  nh13

  authored and

  tfenne

  committed
  4cd5ef9
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Commits on Jun 24, 2016

• Make unzipBlock in BlockGunzipper public. (samtools#650)

  

  nh13

  authored and

  tfenne

  committed
  ec44a54
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Commits on Jun 21, 2016

• Merge pull request samtools#641 from samtools/ak_split_asyncFlags

  akiezun

  authored
  2e26fe8
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• split async flags for read and write

  akiezun

  committed
  f5eb97d
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• Merge pull request samtools#594 from samtools/nh_liftover_helper

  nh13

  authored
  dbee9ac
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