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Commits on Jun 13, 2016

• Modify RevertSam to set the mate unmapped flag properly for single-end data.

  ktibbett

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Commits on May 9, 2016

• Allow RevertSam to optionally output by read group. When run with OUTPUT_BY_READGROUP=true, multiple output bams will be created, each containing the reads for a single read group. Support outputti…

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  Dave Shiga

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Commits on Feb 23, 2016

• squid:S1197 - Array designators [] should be on the type, not the variable

  

  Mohammed Ezzat

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Commits on Jan 7, 2016

• Package-wide documentation improvements

  

  Geraldine Van der Auwera

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Commits on Sep 9, 2015

• Log before you revert so that the logging position stays accurate.

  

  Eric Banks

  committed
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Commits on Sep 1, 2015

• Clear the AS (alignment score) tag as a default.

  ktibbett

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Commits on Dec 10, 2014

• Code review changes.

  jacarey

  committed
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Commits on Dec 9, 2014

• Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes branch of the htsjdk.

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Commits on Oct 22, 2014

• This makes a fundamental change to how we run Picard. We now have a

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  nh13

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Commits on Sep 14, 2014

• Fix so BAMRecordCodec will recognize when qual array has been changed.

  ktibbett

  committed
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Commits on Sep 11, 2014

• Use original qualities to detect encoding scheme if they are being restored.

  ktibbett

  committed
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Commits on Sep 8, 2014

• Modify SANITIZE method of ReverSam to convert all non-Standard quality score encoding schemes to Standard.

  ktibbett

  committed
  8038147

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• Fix issue with VALIDATION_STRINGENCY not being propagated.

  ktibbett

  committed
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Commits on Aug 26, 2014

• Fix oversight in SANITIZE block resulting in NPE if there's only one read group.

  ktibbett

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Commits on Aug 25, 2014

• Modified Casava18ReadNameEncoder to correctly display filter status. Previously it was treated as "passing filter" when in fact Illumina's intended meaning in the read name is "is filtered" (i.e. …

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  ktibbett

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Commits on May 3, 2014

• Step 3: Optimizing imports

  

  Nils Homer

  committed
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• Step 2: refactor files for the split and refactor to produce picard

  

  Nils Homer

  committed
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• Step 1: initial move of files for split and refactor to produce picard

  

  Nils Homer

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