delangel 5992b79159 a) Simplify normalization code in ProduceBeagleInputWalker, as to always normalize, and use MathUtils.normalizeFromLog10 to do this. ... b) Several improvements to BeagleOutputToVCFWalker: 1. If a Hapmap input track is provided (e.g. -B comp,VCF,file), Hapmap sites will be annotated with Hapmap Allele count and allele frequency (key ACH, AFH). 2. If probability of correct genotype is lower than ncthr (optional argument provided by user, default = 0.0), walker will keep original calls instead of using Beagle calls. 3. Instead of annotating just whether Beagle had modified a site, annotate instead HOW MANY genotypes in a site were actually changed by Beagle. All three improvements are mostly for debugging and analysis only. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3769 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-12 19:54:58 +00:00
..
net/sf/picard/reference	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
org	a) Simplify normalization code in ProduceBeagleInputWalker, as to always normalize, and use MathUtils.normalizeFromLog10 to do this.	2010-07-12 19:54:58 +00:00