asivache d603145cb0 Meaning of input arguments has CHANGED: minFraction is now a minimum fraction of CONSENSUS indel observation, out of all reads covering the site, required to make the call. minConsensusFraction is still the minimum fraction of CONSENSUS indel observation out of all indel observations at the site ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1160 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-02 20:38:10 +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	Meaning of input arguments has CHANGED: minFraction is now a minimum fraction of CONSENSUS indel observation, out of all reads covering the site, required to make the call. minConsensusFraction is still the minimum fraction of CONSENSUS indel observation out of all indel observations at the site	2009-07-02 20:38:10 +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