hanna 1f0d852a48 Fix bug where alignments with indels would be busted because bwa reverses ... the read bases to undo a previous read base reverse that doesn't occur in the libbwa codepath. Also fixed some memory management issues. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-29 21:33:13 +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 bug where alignments with indels would be busted because bwa reverses	2009-10-29 21:33:13 +00:00
test/org/broadinstitute/sting	better multi-sample integration test	2009-10-29 13:51:51 +00:00