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CNV
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BCF2 with support symbolic alleles
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2012-06-30 11:22:48 -04:00 |
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annotator
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FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing
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2012-07-18 16:07:47 -04:00 |
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beagle
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Fixing remaining integration test errors. Adding missing ex2.bcf
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2012-06-30 16:23:11 -04:00 |
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bqsr
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Reverting move of BQSR tests to public, as per DR's email
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2012-07-19 10:02:05 -04:00 |
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coverage
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DoC now properly handles reference N bases + misc. additional cleanups
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2012-02-25 11:32:50 -05:00 |
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diagnostics
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Fixing remaining integration test errors. Adding missing ex2.bcf
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2012-06-30 16:23:11 -04:00 |
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diffengine
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Cleanup of VCF header lines and constants, BCF2 bugfixes
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2012-06-21 15:16:31 -04:00 |
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fasta
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Several more walkers have been brought up to use the new Allele representation.
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2012-07-27 02:14:25 -04:00 |
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filters
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Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR
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2012-07-25 08:56:39 -04:00 |
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genotyper
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Remerge after changes to allele construction code. More cleanups/fixes to artificial read pileup provider
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2012-07-30 21:32:03 -04:00 |
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indels
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Cleanup of VCF header lines and constants, BCF2 bugfixes
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2012-06-21 15:16:31 -04:00 |
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phasing
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- Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE
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2012-07-17 15:21:10 -04:00 |
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qc
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First version of VariantContextBuilder
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2011-11-18 11:06:15 -05:00 |
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validation
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Allele refactoring checkpoint #3: all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this.
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2012-07-27 15:48:40 -04:00 |
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varianteval
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Removed the "Walker" suffix from all walkers that had it.
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2012-07-20 17:27:11 -04:00 |
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variantrecalibration
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In ApplyRecalibration marking filter as PASS instead of '.' when the site passes by calling .passFilters().
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2012-07-13 15:40:56 -04:00 |
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variantutils
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With the new Allele representation we can finally handle complex events (because they aren't so complex anymore). One place this manifests itself is with the strict VCF validation (ValidateVariants used to skip these events but doesn't anymore) so I've added a new test with complex events to the VV integration test.
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2012-07-29 19:22:02 -04:00 |
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BAQIntegrationTest.java
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merge master
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2011-10-25 16:08:39 -04:00 |
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ClipReadsWalkersIntegrationTest.java
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Cleanup of VCF header lines and constants, BCF2 bugfixes
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2012-06-21 15:16:31 -04:00 |
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FlagStatIntegrationTest.java
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Adding integration test for Flag Stat
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2012-04-10 22:40:38 -04:00 |
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PileupWalkerIntegrationTest.java
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Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.
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2012-04-02 14:27:36 -04:00 |
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PrintReadsIntegrationTest.java
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Cleanup of VCF header lines and constants, BCF2 bugfixes
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2012-06-21 15:16:31 -04:00 |
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PrintReadsUnitTest.java
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Removed the "Walker" suffix from all walkers that had it.
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2012-07-20 17:27:11 -04:00 |
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