asivache db429e1096 Some alt consenses may have cigar string starting with an insertion. Not a bug, strictly speaking, since the cleaner had been detecting this and crashing deliberately. Now it knows how to deal with this special case though. Also, uppercase the ref before using it in SW aligner! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2722 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-28 18:53:02 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Some alt consenses may have cigar string starting with an insertion. Not a bug, strictly speaking, since the cleaner had been detecting this and crashing deliberately. Now it knows how to deal with this special case though. Also, uppercase the ref before using it in SW aligner!	2010-01-28 18:53:02 +00:00
test/org/broadinstitute/sting	V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository	2010-01-28 18:37:17 +00:00