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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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Removing the legacy -L "interval1;interval2" syntax
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2011-11-21 13:18:53 -05:00 |
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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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Intermediate fix for pool GL unit test: fix up artificial read pileup provider to give consistent data. b) Increase downsampling in pool integration tests with reference sample, and shorten MT tests so they don't last too long
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2012-07-30 09:56:10 -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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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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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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Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants
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2012-07-10 13:59:00 -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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