delangel 422d4ceeea removed useless file - no need for tableRecalibration, right now everything is done in PairHMMIndelErrorModel ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5725 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-02 20:35:44 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	removed useless file - no need for tableRecalibration, right now everything is done in PairHMMIndelErrorModel	2011-05-02 20:35:44 +00:00
test	New visualization output for VQSR. It creates the R script file on the fly and then runs Rscript on it. Adding 1000G Project consensus code. First pass of having VQSR work with missing data by marginalizing over the missing dimension for that data point (thanks Chris and Bob for ideas). Updated math functions to use apache math commons instead of approximations from wikipedia. New parameters available for the priors based on further reading in Bishop and looking at the new visualizations. Updated integration test to use more modern files. Updated MDCP to use new best practices w.r.t. annotations.	2011-05-02 19:14:42 +00:00