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reverting an accidental change from the dindel merge 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4434 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-06 03:08:09 +00:00
parent 28ac1d325e
commit 3d564f4a29
1 changed files with 2 additions and 4 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -164,9 +164,7 @@ public class UnifiedGenotyperEngine {
if ( bestAFguess != 0 ) {
phredScaledConfidence = QualityUtils.phredScaleErrorRate(normalizedPosteriors[0]);
if ( Double.isInfinite(phredScaledConfidence) )
// todo - verify this is OK
phredScaledConfidence = (double)QualityUtils.MAX_QUAL_SCORE;
//phredScaledConfidence = -10.0 * log10AlleleFrequencyPosteriors.get()[0];
phredScaledConfidence = -10.0 * log10AlleleFrequencyPosteriors.get()[0];
} else {
phredScaledConfidence = QualityUtils.phredScaleErrorRate(PofF);
if ( Double.isInfinite(phredScaledConfidence) ) {
@ -230,7 +228,7 @@ public class UnifiedGenotyperEngine {
// todo - temp fix until we can deal with extended events properly
//VariantContext vc = new VariantContext("UG_call", loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);
VariantContext vc = new VariantContext("UG_call", loc.getContig(), loc.getStart(),
Math.max(loc.getStart()+refAllele.length()-1,loc.getStart()),
(refAllele.length() > 0 ? loc.getStart()+refAllele.length()-1 : loc.getStart()),
alleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence, atTriggerTrack) ? null : filter, attributes);