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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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Update MD5s with new FS score
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2012-08-28 08:06:47 -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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Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.
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2012-09-20 14:14:34 -04:00 |
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coverage
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number of stashed changes are lurking in here. In order of importance:
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2012-08-21 07:08:58 -04:00 |
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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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In order to be considered an informative read in the PerReadAlleleLikelihoodMap it has to be informative compared to all other alleles not just the worst allele. Also, fixing a bug when there is only one allele in the map.
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2012-10-18 14:31:15 -04:00 |
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indels
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Allowing the GATK to have non-required outputs
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2012-10-15 13:49:08 -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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In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC.
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2012-08-14 15:02:30 -04:00 |
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variantrecalibration
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Update md5s for VQSR, as VQSLOD is now a double and gets the standard double precision treatment in VCF
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2012-08-30 19:41:49 -04:00 |
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variantutils
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Finalizing IndependentAllelesDiploidExactAFCalc
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2012-10-15 08:21:03 -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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Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig
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2012-09-05 21:10:03 -04:00 |
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PrintReadsIntegrationTest.java
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ReadShard are no longer allowed to span multiple contigs
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2012-08-30 10:15:11 -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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