ebanks 686c8133ed massive change in the way the cleaner works, mostly revolving around the fact ... that we no longer trust indels from the alignments (although we do use it as a good alternate consensus possibility). Other changes include better "greedy mode" performance and allowing the user to have just the cleaned reads themselves be printed out (mostly for Matt's CleanedReadInjector). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1065 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-21 03:56:59 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	massive change in the way the cleaner works, mostly revolving around the fact	2009-06-21 03:56:59 +00:00
test/org/broadinstitute/sting	Cleanup of the cleaned read injector based on Eric's feedback.	2009-06-19 22:04:47 +00:00