depristo 0ad1ea4aa1 Fixed Umapped misspelling ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5196 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-04 22:21:41 +00:00
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bwa	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +00:00
reference	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
Aligner.java	Minor tweak to improve ease-of-use of iterator system.	2009-11-20 18:24:19 +00:00
Alignment.java	Fixed Umapped misspelling	2011-02-04 22:21:41 +00:00
AlignmentValidationWalker.java	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
AlignmentWalker.java	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
CountBestAlignmentsWalker.java	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
package-info.java	Help system content for the alignment module.	2009-12-11 16:01:25 +00:00