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Changed dontRequireSomeSampleHasDoubleAltAllele parameter to mean that merging should only start at a polymorphic site 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4783 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2010-12-03 17:52:56 +00:00
parent ec174dc0ba
commit 4719bbc772
1 changed files with 8 additions and 5 deletions
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13
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.Argument;
@ -99,8 +98,8 @@ public class MergeSegregatingAlternateAllelesWalker extends RodWalker<Integer, I
vcMergeRule = new SameGenePlusWithinDistanceMergeRule(maxGenomicDistance, genomeLocParser, mergeBasedOnRefSeqAnnotation);
VariantContextUtils.AlleleMergeRule alleleMergeRule;
if (dontRequireSomeSampleHasDoubleAltAllele) // if a pair of VariantContext passes the vcMergeRule, then always merge them:
alleleMergeRule = new AlwaysMergeAllelesRule();
if (dontRequireSomeSampleHasDoubleAltAllele) // if a pair of VariantContext passes the vcMergeRule, then always merge them if there is a trailing prefix of polymorphisms (i.e., upstream polymorphic site):
alleleMergeRule = new PrefixPolymorphismMergeAllelesRule();
else
alleleMergeRule = new ExistsDoubleAltAlleleMergeRule();
@ -231,8 +230,12 @@ class SameGenePlusWithinDistanceMergeRule extends DistanceMergeRule {
class AlwaysMergeAllelesRule extends VariantContextUtils.AlleleMergeRule {
class PrefixPolymorphismMergeAllelesRule extends VariantContextUtils.AlleleMergeRule {
public boolean allelesShouldBeMerged(VariantContext vc1, VariantContext vc2) {
return true;
return vc1.isPolymorphic();
}
public String toString() {
return super.toString() + ", there exists a polymorphism at the start of the merged allele";
}
}