delangel 7d7ce6cf00 Two embarassing bug fixes: ... a) Forgot to convert from phred to log-prob when computing gap penalties from recal table. b) Forgot to uncomment code to correctly deal with hard-clipped bases in a read. But because of this, had to do a short term workaround to at least temporarily return class from hardClipAdaptorSequence to GATKSAMRecord. Otherwise, I get exceptions when casting because somehow some reads in HiSeq get to be SAMRecord (which GATKSAMRecord inherits from) but some reads get to be BAMRecords (which can't be cast into GATKSAMRecord), not sure why. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5771 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-05 17:08:34 +00:00
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broadinstitute/sting	Two embarassing bug fixes:	2011-05-05 17:08:34 +00:00