Ryan Poplin 41ffd08d53 On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.		2012-02-13 12:35:09 -05:00
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BAQ.java	Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.	2012-02-03 17:13:52 -05:00
BAQSamIterator.java	On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.	2012-02-13 12:35:09 -05:00