ebanks a0231f073f 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4255 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-12 05:06:37 +00:00
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net/sf/picard/reference	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
org/broadinstitute/sting	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