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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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rpoplin ed08899abc Overwhelming evidence that maxQ = 50 is now a better default than maxQ = 40 in the base quality score recalibrator, especially when combined with dbsnp build 132. Also, added option in ProduceBeagleInputWalker for Beagle-ing chromosome X calls with male samples which sets the genotype likelihood for the AB allele to zero for those samples. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4731 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-24 21:32:26 +00:00
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arguments Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
contexts/variantcontext JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts 2010-11-17 16:08:16 +00:00
datasources Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes. 2010-11-19 19:59:05 +00:00
executive Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
filters Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
iterators Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes. 2010-11-19 19:59:05 +00:00
refdata Change the interface for RMDTrackBuilder, therefore always mandating the specification 2010-11-17 19:00:17 +00:00
traversals Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
walkers Overwhelming evidence that maxQ = 50 is now a better default than maxQ = 40 in the base quality score recalibrator, especially when combined with dbsnp build 132. Also, added option in ProduceBeagleInputWalker for Beagle-ing chromosome X calls with male samples which sets the genotype likelihood for the AB allele to zero for those samples. 2010-11-24 21:32:26 +00:00
WalkerManagerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00