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Supports GQ now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5265 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-17 22:30:25 +00:00
parent 860b172ef1
commit 57c66b5602
1 changed files with 6 additions and 0 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -33,7 +33,9 @@ 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;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.PrintStream;
import java.util.*;
@ -103,6 +105,10 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount() + vc.getHomVarCount()); } });
getters.put("NSAMPLES", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples()); } });
getters.put("NCALLED", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getNSamples() - vc.getNoCallCount()); } });
getters.put("GQ", new Getter() { public String get(VariantContext vc) {
if ( vc.getNSamples() > 1 ) throw new UserException("Cannot get GQ values for multi-sample VCF");
return String.format("%.2f", 10 * vc.getGenotype(0).getNegLog10PError());
}});
}