ebanks 01e73fc39e Yuck - Picard's SAMRecord Comparator only deals with mapped reads. Adding an extended version that works for all reads. ... After adding some more minor changes to the new realigner it now gets the same exact results as the original version - except that sometimes it doesn't clean when it shouldn't! More testing coming. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2731 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-29 07:49:47 +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	Yuck - Picard's SAMRecord Comparator only deals with mapped reads. Adding an extended version that works for all reads.	2010-01-29 07:49:47 +00:00
test/org/broadinstitute/sting	Basic support for very simple index-driven locus traversals. Interface has been changed to	2010-01-29 03:14:26 +00:00