From cdc175f7e3a05a272b62af251c542919700d8965 Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 20 Apr 2010 17:41:52 +0000 Subject: [PATCH] Synchronizing version to make sure everything compiles; this model is not operational yet git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3214 348d0f76-0448-11de-a6fe-93d51630548a --- .../SimpleIndelCalculationModel.java | 20 ++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java index 563a4cce8..c210d568d 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java @@ -16,15 +16,29 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel { protected SimpleIndelCalculationModel() {} + private int testSkipCount = 5; + public VariantCallContext callLocus(RefMetaDataTracker tracker, char ref, GenomeLoc loc, Map contexts, DiploidGenotypePriors priors) { cachedContext = contexts; return null; } - public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char ref, GenomeLoc loc, Map contexts) { - - System.out.println("Reached " + loc + " through an extended event"); + public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char[] ref, GenomeLoc loc, Map contexts) { + System.out.println("\nReached " + loc + " through an extended event"); + for (Map.Entry e : contexts.entrySet()) { + System.out.println("Set "+e.getKey()); + System.out.println(" Context: "+e.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size()+ " reads"); + System.out.println(" Cached context: "+ + cachedContext.get(e.getKey()).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size()+ " reads"); + System.out.println(" First read in cached context: "+ + cachedContext.get(e.getKey()).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup().getReads().get(0).getReadName()); + ReadBackedExtendedEventPileup p = e.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getExtendedEventPileup(); + if ( p== null ) System.out.println("EXTENDED PILEUP IS NULL"); + System.out.println(" Event(s): " + e.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getExtendedEventPileup().getEventStringsWithCounts(ref)); + } + if ( testSkipCount==0 ) System.exit(1); + testSkipCount--; // TODO -- implement me //VariantContext vc = new MutableVariantContext("UG_indel_call", loc, alleles, genotypes, phredScaledConfidence/10.0, null, attributes);