delangel d534241f35 Major revamp of annotations for indels: ... a) All rank sum tests now work for indels including multiallelic sites. For the latter cases, rank sum test is REF vs most common allele b) Redid computation of HaplotypeScore for indels. It's now trivially easy to do because we are already computing likelihoods of each read vs haplotypes in GL computation so we reuse that if available. For multiallelic case, we score against N haplotypes where N is total called alleles. Drawback is that all cases need information contained in likelihood table that stores likelihood for each pileup element, for each allele. If this table is not available we dont annotate, so we can only fully annotate indels right now when running UG but not when running VariantAnnotator alone. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5947 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-04 15:34:24 +00:00
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net/sf	A fix for Marian Thieme's NPE in the new sharding system.	2011-04-21 19:47:14 +00:00
org/broadinstitute/sting	Major revamp of annotations for indels:	2011-06-04 15:34:24 +00:00