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annotator
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When you commit code late at night you tend to make careless mistakes... like forgetting to update integration tests.
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2010-11-12 14:41:10 +00:00 |
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beagle
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The dev team has decided to change the filter that is added to records that are set to monomorphic by Beagle. It no longer lists the reference allele. Added those filters to the header of the output VCF file. Finally, we no longer use R2=NaN values coming from Beagle.
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2010-11-30 17:19:54 +00:00 |
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coverage
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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fasta
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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filters
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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genotyper
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Fare thee well, UGv1. Here come the days UGv2.
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2010-11-29 21:51:19 +00:00 |
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indels
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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phasing
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Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was previously 20)
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2010-12-03 16:31:13 +00:00 |
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qc
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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recalibration
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Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.
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2010-12-02 18:43:24 +00:00 |
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sequenom
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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varianteval
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Passing ReviewedStingExceptions through the HMS.
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2010-11-16 21:50:42 +00:00 |
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variantrecalibration
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We no longer look at by-hapmap validation status in the VQSR because using the HapMap VCF file is higher quality. As a side effect we now support the dbsnp 132 vcf file. ApplyVariantCuts now requires that the input VCF rod bindings begin with input, matching the other VQSR walkers. Wiki updated with information about how to obtain the hapmap and 1kg truth sets.
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2010-12-02 15:38:45 +00:00 |
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variantutils
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Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore.
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2010-11-26 18:40:34 +00:00 |
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ClipReadsWalkersIntegrationTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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PileupWalkerIntegrationTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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PrintReadsWalkerUnitTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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VariantsToVCFIntegrationTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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