depristo 5265f943b0 phasing per sample. tmp checkin ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4898 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-22 20:14:06 +00:00
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qscript	phasing per sample. tmp checkin	2010-12-22 20:14:06 +00:00
src	PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).	2010-12-22 15:16:15 +00:00
test/org/broadinstitute/sting/queue	Updated pipeline test to match Eric's changes in r4846.	2010-12-17 19:52:09 +00:00