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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
This commit is contained in:
asivache 2010-04-20 17:41:52 +00:00
parent 4437456bb5
commit cdc175f7e3
1 changed files with 17 additions and 3 deletions
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20
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
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@ -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<String, StratifiedAlignmentContext> contexts, DiploidGenotypePriors priors) {
cachedContext = contexts;
return null;
}
public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> contexts) {
System.out.println("Reached " + loc + " through an extended event");
public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char[] ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> contexts) {
System.out.println("\nReached " + loc + " through an extended event");
for (Map.Entry<String,StratifiedAlignmentContext> 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);