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boneheaded mistake, mixed up my min and max 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5271 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-02-18 04:02:14 +00:00
parent acad3ada06
commit 1bc5c7e99b
1 changed files with 5 additions and 9 deletions
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14
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -27,7 +27,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
int run; int run;
if ( vc.isSNP() ) { if ( vc.isSNP() ) {
run = computeHomopolymerRun(vc.getAlternateAllele(0).getBases()[0], ref, true); run = computeHomopolymerRun(vc.getAlternateAllele(0).getBases()[0], ref);
} else if ( vc.isIndel() && ANNOTATE_INDELS ) { } else if ( vc.isIndel() && ANNOTATE_INDELS ) {
run = computeIndelHomopolymerRun(vc,ref); run = computeIndelHomopolymerRun(vc,ref);
} else { } else {
@ -45,7 +45,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
public boolean useZeroQualityReads() { return false; } public boolean useZeroQualityReads() { return false; }
private static int computeHomopolymerRun(byte altAllele, ReferenceContext ref, boolean domin) { private static int computeHomopolymerRun(byte altAllele, ReferenceContext ref) {
// TODO -- this needs to be computed in a more accurate manner // TODO -- this needs to be computed in a more accurate manner
// We currently look only at direct runs of the alternate allele adjacent to this position // We currently look only at direct runs of the alternate allele adjacent to this position
@ -70,11 +70,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
rightRun++; rightRun++;
} }
if (domin) return Math.max(leftRun, rightRun);
return Math.min(leftRun, rightRun);
else
return Math.max(leftRun, rightRun);
} }
private static int computeIndelHomopolymerRun(VariantContext vc, ReferenceContext ref) { private static int computeIndelHomopolymerRun(VariantContext vc, ReferenceContext ref) {
@ -91,7 +87,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
} }
} }
return computeHomopolymerRun(dBase, ref, false); // do max in both directions return computeHomopolymerRun(dBase, ref);
} else { } else {
// check that inserted bases are the same // check that inserted bases are the same
byte insBase = vc.getAlternateAllele(0).getBases()[0]; byte insBase = vc.getAlternateAllele(0).getBases()[0];
@ -101,7 +97,7 @@ public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
} }
} }
return computeHomopolymerRun(insBase,ref, false); return computeHomopolymerRun(insBase,ref);
} }
} }
} }