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gatk-3.8/java/src/org/broadinstitute/sting/alignment
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aaron 790d2a7776 adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-03 15:56:44 +00:00
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bwa Misc bug fixes. 2010-01-05 14:48:19 +00:00
reference Misc bug fixes. 2010-01-05 14:48:19 +00:00
Aligner.java Minor tweak to improve ease-of-use of iterator system. 2009-11-20 18:24:19 +00:00
Alignment.java BWA: odds and ends. Get rid of some spurious debug code that was accidentally 2009-11-22 15:26:07 +00:00
AlignmentValidationWalker.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
AlignmentWalker.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
CountBestAlignmentsWalker.java adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 2010-03-03 15:56:44 +00:00
package-info.java Help system content for the alignment module. 2009-12-11 16:01:25 +00:00