From 08be871309ecd8959e0cacf8873e21ab56de5d9a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 13 Aug 2013 15:27:17 -0400 Subject: [PATCH] Removing unused code in VariantsToTable: GQ is not an INFO field and is taken care of by -GF and not -F. --- .../sting/gatk/walkers/variantutils/VariantsToTable.java | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index f1f93f1f5..3fcabdf5b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -124,7 +124,7 @@ public class VariantsToTable extends RodWalker { /** * -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 genotypeFieldsToTake = new ArrayList(); @@ -448,10 +448,6 @@ public class VariantsToTable extends RodWalker { 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) {