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Commits on Aug 30, 2012

• Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

  

  Ryan Poplin

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Commits on Aug 29, 2012

• Be careful with String manipulation when constructing alleles in SomaticIndelDetector

  eitanbanks

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Commits on Aug 27, 2012

• LIBS is totally busted for deletions. Putting a check in AD for bad pileup event bases so that we don't produce busted alleles. We must fix LIBS ASAP.

  eitanbanks

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Commits on Aug 25, 2012

• Usability cleanup for BQSR

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  Mark DePristo

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Commits on Aug 24, 2012

• Fixing typo in error message.

  

  Ryan Poplin

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Commits on Aug 22, 2012

• Bug fix for popular _Duplicate allele added to VariantContext_ error reported on the forum. It seems to be due to lower case bases in the reference being treated as reference mismatches. We would t…

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  Ryan Poplin

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• WTF - why is support for whole-read insertions all messed up in LIBS? I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be bette…

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  eitanbanks

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Commits on Aug 21, 2012

• Fix for Adam K's reported bug: we weren't handling reads that were entirely insertions properly in LIBS. Specifically, the event bases were off-by-one (which was disasterous in Adam's case with a 1…

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  eitanbanks

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• Merge remote-tracking branch 'unstable/master'

  eitanbanks

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Commits on Aug 20, 2012

• Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

  

  Ryan Poplin

  committed
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• Pulling out common caller arguments into its own StandardCallerArgumentCollection base class so that every caller isn't exposed to the unused arguments from every other caller.

  

  Ryan Poplin

  committed
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• Fixing the docs for DP and AD

  eitanbanks

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• Bug fix in HaplotypeCaller for non-regular bases in the reference or reads. Those events don't get created any more. Bug fix for advanced GenotypeFullActiveRegion mode: custom variant annotations c…

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  Ryan Poplin

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• Temporarily disabling multi-threaded usage of BaseRecalibrator for performance reasons.

  eitanbanks

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• Thanks to Guillermo I was able to isolate an instance of where the MLEAC > AN. It turns out that this is valid, e.g. when PLs are all 0s for a sample we no-call it but it's allowed to factor into t…

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  eitanbanks

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Commits on Aug 19, 2012

• Print "Parsing data stream with BCF version BCFx.y" in BCF2 codec as .debug not .info

  

  Mark DePristo

  committed
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• CombineVariants outputs the first non-MISSING qual, not the maximum

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  Mark DePristo

  committed
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• Bring bamboo performance test runner script under version control

  droazen

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Commits on Aug 18, 2012

• Cleanup and expansion of GATKPerformanceOfTime

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  Mark DePristo

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Commits on Aug 17, 2012

• Updated and more thorough version of the BadCigar read filter

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  Mauricio Carneiro

  committed
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• Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.

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  Mark DePristo

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• Put in a sanity check that MLEAC <= AN

  eitanbanks

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• Add support for CombineVariants nt option in GATKPerformanceOverTime

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  Mark DePristo

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• Fix for missing formatter in R 2.15

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  Mark DePristo

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• Print to logger not to System.out in CachingIndexFastaSequenceFile when profiling cache performance

  

  Mark DePristo

  committed
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• Fixed GSA-434: GATK should generate error when gzipped FASTA is passed in.

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  Mark DePristo

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• Fixed: GSA-392 @arguments with just a short name get the wrong argument bindings

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  Mark DePristo

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• Potential fix for GSA-484: Incomplete writing of temp BCF when running CombineVariants in parallel

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  Mark DePristo

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• Proper function call in BCF2Decoder to validateReadBytes

  

  Mark DePristo

  committed
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• Bugfix for potential SEGFAULT with JNA getting execution hosts for LSF with multiple hosts

  

  Mark DePristo

  committed
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• Improvements to GATKPerformanceOverTime

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  Mark DePristo

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• Hmm, not good. Fixing the math in PBT resulted in changed MD5s for integration tests that look like significant changes. I am reverting and will report this to Laurent.

  eitanbanks

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• Better error message for reads that begin/end with a deletion in LIBS

  eitanbanks

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Commits on Aug 16, 2012

• GSA-483: Bug in GATKdocs for Enums

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  Mark DePristo

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• FindBugs 'Maintainability' fixes

  eitanbanks

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