asivache 177d6d00b8 added setContigIndex(). NOTE: both setContig() and setContigIndex are UNSAFE as one does not automatically involve updating the other, and there's also no validation ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1130 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-30 17:40:37 +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	added setContigIndex(). NOTE: both setContig() and setContigIndex are UNSAFE as one does not automatically involve updating the other, and there's also no validation	2009-06-30 17:40:37 +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.	2009-06-29 20:51:55 +00:00