ebanks 42c71b4382 Fix for Kris: now SNPs aren't masked by default (only when they come from a mask rod) and we can design Sequenom validation assays for them. ... I'll move this all to core in a bit... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1532 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-04 14:52:06 +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/org/broadinstitute/sting	Fix for Kris: now SNPs aren't masked by default (only when they come from a mask rod) and we can design Sequenom validation assays for them.	2009-09-04 14:52:06 +00:00
test/org/broadinstitute/sting	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00