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annotator
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Expanding the HaplotypeCaller integration tests to cover a wider range of data
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2012-08-22 14:18:44 -04:00 |
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beagle
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FindBugs 'Efficiency' fixes
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2012-08-16 15:40:52 -04:00 |
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bqsr
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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2012-08-21 10:21:47 -04:00 |
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coverage
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Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers.
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2012-07-25 21:40:28 -04:00 |
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diagnostics
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FindBugs 'Maintainability' fixes
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2012-08-16 15:53:06 -04:00 |
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diffengine
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FindBugs 'Maintainability' fixes
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2012-08-16 15:53:06 -04:00 |
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fasta
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Fixed bug in FastaAlternateReferenceMaker when input VCF has overlapping deletions as reported a while back on GS
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2012-08-01 10:45:04 -04:00 |
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filters
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Adding extraDocs tag per Mauricio's request
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2012-07-25 18:23:18 -04:00 |
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genotyper
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Fixing merge conflicts
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2012-08-20 20:38:25 -04:00 |
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indels
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Fix merge conflicts
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2012-08-16 20:45:52 -04:00 |
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phasing
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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.
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2012-08-16 21:41:18 -04:00 |
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qc
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Adding categories for the remaining uncategorized walkers
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2012-07-30 11:35:08 -04:00 |
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validation
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Bugfix for incorrect allele counting in IndelSummary
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2012-08-01 15:45:12 -04:00 |
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varianteval
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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 the MLE (since that's the contract with the exact model). Removing the check in UG and instead protecting for it in the AlleleCount stratification.
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2012-08-20 01:16:23 -04:00 |
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variantrecalibration
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Updating the checkType() function to include the new StructuralIndel variant type. Fixes outstanding broken integration test.
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2012-08-22 07:33:10 -07:00 |
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variantutils
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Docs for --keepOriginalAC were wrong in SelectVariants
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2012-08-22 13:07:13 -04:00 |
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ActiveRegionExtension.java
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Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.
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2012-04-17 14:22:48 -04:00 |
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ActiveRegionWalker.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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Allows.java
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Attribution.java
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BAQMode.java
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By.java
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ClipReads.java
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Quick pass of FindBugs 'should be static inner class' fixes.
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2012-08-08 14:42:06 -04:00 |
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DataSource.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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Downsample.java
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DuplicateWalker.java
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FlagStat.java
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Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers.
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2012-07-25 21:40:28 -04:00 |
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LocusWalker.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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Multiplex.java
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Multiplexer.java
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PartitionBy.java
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PartitionType.java
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Pileup.java
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Better docs for verbose output of Pileup
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2012-08-15 21:55:08 -04:00 |
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PrintRODs.java
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Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers.
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2012-07-25 21:40:28 -04:00 |
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PrintReads.java
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Adding extraDocs tag per Mauricio's request
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2012-07-25 18:23:18 -04:00 |
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RMD.java
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ReadFilters.java
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ReadPairWalker.java
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ReadWalker.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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RefWalker.java
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Fix GSA-137: Having both DataSource.REFERENCE and DataSource.REFERENCE_BASES is confusing to end users.
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2012-08-17 14:55:38 -04:00 |
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Reference.java
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RemoveProgramRecords.java
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Add a RemoveProgramRecords annotation
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2012-08-03 09:54:16 -04:00 |
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Requires.java
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RodWalker.java
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SplitSamFile.java
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Added category docs for the remaining public walkers (I think I got them all). I removed a couple of totally unnecessary walkers.
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2012-07-25 21:40:28 -04:00 |
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TreeReducible.java
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Walker.java
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Few category changes
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2012-07-25 17:23:02 -04:00 |
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WalkerName.java
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Window.java
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package-info.java
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63213e8eb5