asivache f2b3fa83ac fix for another bug found by Eric: some indels were printed into the output stream twice (when there's another indel within MISMATCH_WINDOW bases and that other indel requires delayed print in order to accumulate coverage) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1318 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-27 15:07:07 +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	fix for another bug found by Eric: some indels were printed into the output stream twice (when there's another indel within MISMATCH_WINDOW bases and that other indel requires delayed print in order to accumulate coverage)	2009-07-27 15:07:07 +00:00
test/org/broadinstitute/sting	Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers.	2009-07-24 19:44:04 +00:00