chartl 7c9ef59d65 This is simultaneously a minor and major change to VariantEval, so take heed: ... The core walker has been modified so that when variant contexts (eval and comp) are subset to command-line-specified sample(s), the chromosome count annotations (AC/AN/AF) are altered to reflect the AC/AN/AF of only those samples involved in the comparison. No more getting AC500 when you're comparing a 10-sample overlap. Interestingly enough, this didn't break any integration tests. GenotypeConcordance now has two additional tables: Allele Count Statistics, and Allele Count Summary Statistics. These work exactly identically to the Sample Statistics and Sample Summary Statistics tables, except that the partition being used is no longer the sample, but instead the allele count of the variant sites. These tables stratify by both eval and comp ACs, e.g. evalAC0 evalAC1 evalAC2 compAC0 compAC1 compAC2 Differences with previous integration tests were verified to only be in the Allele Count tables (by grepping them out of the diff); a new test has been added for the simple case of an AC=1 site in the eval becoming an AC=2 site in the comp. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4491 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-13 22:26:15 +00:00
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net/sf/picard/reference	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
org/broadinstitute/sting	This is simultaneously a minor and major change to VariantEval, so take heed:	2010-10-13 22:26:15 +00:00