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print out ref/alt ratio, not major/minor 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1384 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-05 16:36:25 +00:00
parent 48713e154c
commit 3b74b3ba74
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECAlleleBalance.java
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@ -52,10 +52,10 @@ public class VECAlleleBalance implements VariantExclusionCriterion { //extends
int aCount = Utils.countOccurrences(a, bases.toUpperCase());
int bCount = Utils.countOccurrences(b, bases.toUpperCase());
int major = Math.max(aCount, bCount);
int minor = Math.min(aCount, bCount);
int refCount = a == ref ? aCount : bCount;
int altCount = a == ref ? bCount : aCount;
return new Pair(major, minor);
return new Pair(refCount, altCount);
}
public void compute(char ref, AlignmentContext context, rodVariants variant) {
@ -63,7 +63,7 @@ public class VECAlleleBalance implements VariantExclusionCriterion { //extends
Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
int n = counts.first + counts.second;
ratio = counts.first.doubleValue() / (double)n;
exclude = GenotypeUtils.isHet(variant) && ((1.0 - ratio) < lowThreshold || ratio > highThreshold);
exclude = GenotypeUtils.isHet(variant) && (ratio < lowThreshold || ratio > highThreshold);
}
public boolean useZeroQualityReads() { return false; }
@ -73,7 +73,7 @@ public class VECAlleleBalance implements VariantExclusionCriterion { //extends
}
public String getStudyHeader() {
return "AlleleBalance("+lowThreshold+","+highThreshold+")\tMajorRatio";
return "AlleleBalance("+lowThreshold+","+highThreshold+")\tRefRatio";
}
public String getStudyInfo() {