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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alignment	Fixed Umapped misspelling	2011-02-04 22:21:41 +00:00
analyzecovariates	It was returning 1 when it should return 0	2011-03-31 20:50:38 +00:00
commandline	Removed -debug/--debug_mode.	2011-04-27 10:56:39 +00:00
datasources/pipeline	FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait.	2011-02-17 19:09:03 +00:00
gatk	Major revamp of annotations for indels:	2011-06-04 15:34:24 +00:00
jna	Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays.	2011-03-10 22:58:54 +00:00
oneoffprojects	A VariantContext can now be isSymbolic. More importantly, multi-allelic variants are now properly handled in determining their type [using isMixed only if any of the biallelic variant types differ between the alt alleles].	2011-06-03 18:02:47 +00:00
playground	More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.	2011-06-03 20:11:31 +00:00
queue	Somehow checked in a version that was building extensions for everything ("") instead of selected packages. Fixed.	2011-05-16 16:58:37 +00:00
utils	Oops, just realized that I forgot to comment my commit from yesterday so it was clear what was happening	2011-06-03 18:06:41 +00:00