chartl 2235245af0 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). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4894 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-22 15:16:15 +00:00
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old	Restructuring my qscripts	2010-12-11 20:58:45 +00:00
RefineGenotypesAndMerge.q	Commit for Ryan	2010-10-05 19:04:10 +00:00
batchMergePipeline.q	Now that addAll() is in the superclass, no longer need this definition (which, without override, prevents the script from compiling anyway)	2010-12-17 05:36:31 +00:00
expanded_targets.q	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
fullCallingPipelineV2.q	java changes:	2010-12-12 05:10:45 +00:00
omni_qc.q	Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.	2010-11-03 19:23:03 +00:00
private_mutations.q	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