chartl c9d473edee More changes to Variant Eval and Genotype Concordance (passes all integration tests): ... 1: -sample can now include a file, which will be parsed for sample-name entries 2: If you request a sample to run analysis on, but it is not present in any of your RODs, VEW will exception out 3: Change added to parse Integer, String, and List<Integer> type Allele Count annotations (error otherwise) 4 [slightly problematic]: The count objects now maintain row-keys in order, as the keys were taking an inordinate amount of time in onTraversalDone (multiple calls to getRowKeys(), so many multiple sorts of the same underlying unsorted object, very bad) There is a legacy comparison object which is unused which I will strip out soon. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4502 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-15 12:40:36 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	More changes to Variant Eval and Genotype Concordance (passes all integration tests):	2010-10-15 12:40:36 +00:00
test	Adding an integration test (against hg18 this time) that requires on-the-fly sorting in order to work properly.	2010-10-15 07:45:21 +00:00