jmaguire 4019cd2bd7 Added ROD for parsing hapmap3 genotype files. ... Tweak to TabularROD to allow HapMapGenotypeROD to work. Added HapMapGenotypeROD to list of RODs in ReferenceOrderedData.java. Modified MultiSampleCaller to return a single object with most of the relvant information. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1169 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-05 16:28:24 +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	Added ROD for parsing hapmap3 genotype files.	2009-07-05 16:28:24 +00:00
test/org/broadinstitute/sting	When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!	2009-07-02 14:15:50 +00:00