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Removing min confidence for on/off genotype 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1473 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-08-28 01:04:13 +00:00
parent 4f7ed69242
commit f0179109fa
1 changed files with 1 additions and 4 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java
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@ -5,8 +5,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.*;
public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // extends RatioFilter {
private static final double minGenotypeConfidenceToTest = 5.0; // TODO -- must be replaced with true confidence scoore, right now assumes LOD
//final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.LeftTailed;
private boolean exclude;
private double threshold = 0.0;
@ -53,8 +51,7 @@ public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // ext
Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
int n = counts.first + counts.second;
ratio = counts.first.doubleValue() / (double)n;
boolean highGenotypeConfidence = variant.getConsensusConfidence() > minGenotypeConfidenceToTest;
exclude = ratio < threshold && highGenotypeConfidence;
exclude = ratio < threshold;
}
public double inclusionProbability() {