From bb86c0e03a9b97bb4d77c22b7ba78823465a6410 Mon Sep 17 00:00:00 2001 From: weisburd Date: Tue, 18 May 2010 02:43:13 +0000 Subject: [PATCH] Improved error message git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/annotator/GenomicAnnotation.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java index 555f2ce46..712d11efa 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java @@ -15,7 +15,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.refdata.AnnotatorROD; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.TabularROD; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; @@ -109,7 +108,7 @@ public class GenomicAnnotation implements InfoFieldAnnotation { //continue; //TODO If this site is monomorphic in the VC, and the current record specifies a particular alternate allele, skip this record. Right? //} else if(alternateAlleles.size() > 1) { - throw new StingException("Record (" + rod + ") in " + name + " contains " + alternateAlleles.size() + " alternate alleles. GenomicAnnotion currently only supports annotating 1 alternate allele."); + throw new StingException("Record [" + vc + "] contains " + alternateAlleles.size() + " alternate alleles. GenomicAnnotion currently only supports annotating 1 alternate allele."); } boolean positiveStrand = true; //if HAPLOTYPE_STRAND_COLUMN isn't specified, assume positive strand. @@ -157,7 +156,6 @@ public class GenomicAnnotation implements InfoFieldAnnotation { //match against hapolotypeReference. Allele vcRef = vc.getReference(); if(!vcRef.basesMatch(hapRefValue)) { - //TODO check the intersection of vcRef and hapRefValue continue; //skip record } }