hanna 83b8676b69 Hack to fix mysterious disappearing read attributes. Ultimately caused ... by the fact that the GATKSAMRecord, by design, needs to both inherit from SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't implemented as explicit passthroughs can compromise the content of the SAMRecord in subtle ways. Will be automatically fixed when Picard moves to a lightweight SAMRecord interface rather than the current heavyweight implementation. But in the short-term, there's no obvious fix. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-13 19:06:54 +00:00
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IndelRealignerIntegrationTest.java	Hack to fix mysterious disappearing read attributes. Ultimately caused	2010-10-13 19:06:54 +00:00
IndelRealignerPerformanceTest.java	Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test.	2010-09-12 05:06:37 +00:00
RealignerTargetCreatorIntegrationTest.java	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
RealignerTargetCreatorPerformanceTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00