aaron a6d3e4bd47 Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes). ... This check-in will temperarly break the build (I need to see if Bamboo is correctly returning the log file for the failed builds). Will be fixed once Bamboo starts building. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3609 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-22 18:26:37 +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	Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes).	2010-06-22 18:26:37 +00:00
test/org/broadinstitute/sting	Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes).	2010-06-22 18:26:37 +00:00