After viewing results on real case/control data from RAW -- it's really working quite well. ReadIndels, however, needs to use a T-test rather than a U-test, especially in deep coverage (at indel sites, the reads with indels will have mostly the same number of CIGAR indel elements -- one -- which doesn't really play nicely with the UTest when sample sets are large). Modified ReadsLargeInsertSize to be a two-way test (e.g. ReadsLarge and ReadsSmall). BaseQualityScore also suffers from the same issue as read indels, so switching over to a T-test in that case as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5653 348d0f76-0448-11de-a6fe-93d51630548a
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