ebanks ba8a8febc6 Thanks to Steve Hershman for finding this bug: ... getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled). Probably we should change the method to be getNeg10Log10PError(). Anyone have strong feelings on this? git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-02 01:59:03 +00:00
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varianteval	Thanks to Steve Hershman for finding this bug:	2009-12-02 01:59:03 +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
ConcordanceTruthTableTest.java	adding an extra bit of data to come out of CTT (number of chips with actual data)	2009-11-19 17:46:10 +00:00
HapmapPoolAllelicInfoIntegrationTest.java	oops forgot to update the md5s	2009-11-19 18:22:29 +00:00