Mark DePristo 5ec25797b3 Optimizations for BaseRecalibrator ... -- No longer computes at each update the overall read group table. Now computes this derived table only at the end of the computation, using the ByQual table as input. Reduces BQSR runtime by 1/3 in my test		2012-12-17 16:47:27 -05:00
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src/org/broadinstitute/sting	Optimizations for BaseRecalibrator	2012-12-17 16:47:27 -05:00
test/org/broadinstitute/sting	Changing the HC over to using the non-contamination-downsampled read maps for the purposes of annotations. This behavior now matches the UG. There is a new command line option to go back to the older behavior to explore the differences.	2012-12-17 11:27:44 -05:00