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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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chartl 42e9987e69 Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array. 
Bug fix to LiftoverVariants - no barfing at reference sites.

AlleleFrequencyComparison - local changes added to make sure parsing works properly

Added HammingDistance annotation. Mostly useless. But only mostly.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4622 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-03 19:23:03 +00:00
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annotator Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
beagle Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
coverage Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
fasta Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
filters Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
genotyper Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
indels Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
phasing Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
qc Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
recalibration Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
sequenom Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
varianteval Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array. 2010-11-03 19:23:03 +00:00
variantrecalibration Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
variantutils Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
ClipReadsWalkersIntegrationTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
PileupWalkerIntegrationTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
PrintReadsWalkerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
VariantsToVCFIntegrationTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00