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Removing unused code in VariantsToTable: GQ is not an INFO field and is taken care of by -GF and not -F.

This commit is contained in:
Eric Banks 2013-08-13 15:27:17 -04:00
parent 17eb7b49fe
commit 08be871309
1 changed files with 1 additions and 5 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -124,7 +124,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
/**
* -GF NAME can be any binding in the FORMAT field (e.g., GQ, PL).
* Note this argument accepts any number of inputs. So -F GQ -F PL is allowed.
* Note this argument accepts any number of inputs. So -GF GQ -GF PL is allowed.
*/
@Argument(fullName="genotypeFields", shortName="GF", doc="The name of each genotype field to capture for output in the table", required=false)
public List<String> genotypeFieldsToTake = new ArrayList<String>();
@ -448,10 +448,6 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
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("MULTI-ALLELIC", new Getter() { public String get(VariantContext vc) { return Boolean.toString(vc.getAlternateAlleles().size() > 1); } });
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).getLog10PError());
}});
}
private static Object splitAltAlleles(VariantContext vc) {