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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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I forget why I thought that the VariantAnnotator couldn't run multi-threaded because it works just fine. Now you can specify -nt with VA.
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2012-11-26 11:34:59 -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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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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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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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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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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Fixing md5s to reflect the new HapMap file
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2012-10-30 14:27:10 -04:00 |
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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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change the md5 in one of the CV intergration tests, since it wasn't use the priority list when printing the origin of the annotation (the setValue field)
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2012-12-10 22:48:15 -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 |
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