Mark DePristo a481d006f0 Optimizations for applying BQSR table with PrintReads ... -- Cleaned up code in updateDataForRead so that constant values where not computed in inner loops -- BaseRecalibrator doesn't create it's own fasta index reader, it just piggy backs on the GATK one -- ReadCovariates <init> now uses a thread local cache for it's int[][][] keys member variable. This stops us from recreating an expensive array over and over. In order to make this really work had to update recordValues in ContextCovariate so it writes 0s over base values its skipping because of low quality base clipping. Previously the values in the ReadCovariates keys were 0 because they were never modified by ContextCovariates. Now these values are actually zero'd out explicitly by the covariates.		2012-12-17 16:47:27 -05:00
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src/org/broadinstitute/sting	Optimizations for applying BQSR table with PrintReads	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