ebanks fcce77c245 Added -beagle option to emit likelihoods file for use with the BEAGLE imputation engine; still experimental. ... (Also converted getPileup -> getBasePileup) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2549 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-08 18:41:04 +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	Added -beagle option to emit likelihoods file for use with the BEAGLE imputation engine; still experimental.	2010-01-08 18:41:04 +00:00
test/org/broadinstitute/sting	Bug fixes for both SET_Q_ZERO and REMOVE_REF_BIAS solid recal modes regarding proper handling of negative strand reads. These changes yield a minor improvment in HapMap sensitivity.	2010-01-08 15:19:22 +00:00