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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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QD is now divided by the average length of the alternate allele (weighted by the allele count). The average length is stored in a related annotation, "AAL", which can be used to re-compute the "old" QD by simple multiplication. Integration tests *should* all pass.
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2013-01-02 14:41:29 -05:00 |
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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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Fix bugs as reported on the forum: BED needs to be explicitly set as the default output format and the output didn't actually adhere to the BED spec.
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2012-11-08 15:07:47 -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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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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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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Fixing problem reported on forum for VF: DP couldn't be filtered from the FORMAT field, only from the INFO field. Fixed and added integration test.
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2012-10-26 00:57:40 -04:00 |
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genotyper
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ArtificialReadPileupTestProvider now creates GATKSamRecords with good header values
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2012-12-24 13:35:57 -05:00 |
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indels
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Allow large-scale tests 5 hours each to run
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2012-11-01 17:48:58 -04:00 |
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phasing
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Fix for PBT bug reported on the forum: the AD is actually output correctly now (rather than with 'null' or some gibberish memory pointer).
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2012-12-13 23:28:30 +00:00 |
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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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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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variantrecalibration
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Fixing md5s to reflect the new HapMap file
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2012-10-30 14:27:10 -04:00 |
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variantutils
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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package
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2012-12-19 10:25:22 -05:00 |
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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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some changes.
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2012-12-14 17:21:32 -05:00 |
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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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PrintReadsLargeScaleTest.java
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PrintReads large-scale test to protect against another major low-level performance issue
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2012-12-05 21:36:27 -05:00 |
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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 |
e1d09ab0db