Mauricio Carneiro c210b7cde4 Merge GATK repo into CMI-GATK ... Bringing in the following relevant changes: * Fixes the indel realigner N-Way out null pointer exception DEV-10 * Optimizations to ReduceReads that bring the run time to 1/3rd. Conflicts: protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java DEV-10 #resolve #time 2m		2012-10-23 10:59:11 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Merge GATK repo into CMI-GATK	2012-10-23 10:59:11 -04:00
test	Updating MD5s for confidence ref site estimation in IndependentAllelesDiploidExactAFCalc	2012-10-23 06:47:53 -04:00