depristo a8a2c1a2a1 Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1882 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-20 01:19:58 +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	Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads	2009-10-20 01:19:58 +00:00
test/org/broadinstitute/sting	Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this.	2009-10-19 21:54:53 +00:00