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VariantsToTable now supports the virtual TRANSITION field 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4558 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-10-22 19:53:46 +00:00
parent 9fcfd8fa0d
commit 78b4a1c240
1 changed files with 7 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
@ -87,6 +88,12 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
}
});
getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } });
getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) {
if ( vc.isSNP() && vc.isBiallelic() )
return VariantContextUtils.isTransition(vc) ? "1" : "0";
else
return "-1";
}});
getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
});