chartl be31d7f4cc Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it. ... This will output for hapmap variant sites: chromosome position ref allele variant allele number of variant alleles of the individuals depth of coverage power to detect singletons at lod 3 number of variant bases seen whether or not variant was called git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2068 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-18 15:47:52 +00:00
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varianteval	-Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out).	2009-11-01 05:35:47 +00:00
variantstovcf	changes to VCF output, and updated MD5's in the integration tests	2009-10-14 18:42:48 +00:00
BaseTransitionTableCalculatorJavaIntegrationTest.java	BTTJ is now correct. What a terrible waste of time, turns out I'd just reversed the header. Because of this the MD5 had to be updated in the tests.	2009-10-26 19:24:18 +00:00
ClipReadsWalkersIntegrationTest.java	Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this.	2009-10-19 21:54:53 +00:00
HapmapPoolAllelicInfoIntegrationTest.java	Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it.	2009-11-18 15:47:52 +00:00