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Improved error message 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-05-18 02:43:13 +00:00
parent 68719615be
commit bb86c0e03a
1 changed files with 1 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java
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@ -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.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.AnnotatorROD; import org.broadinstitute.sting.gatk.refdata.AnnotatorROD;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.TabularROD;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; 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? //continue; //TODO If this site is monomorphic in the VC, and the current record specifies a particular alternate allele, skip this record. Right?
//} else //} else
if(alternateAlleles.size() > 1) { 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. 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. //match against hapolotypeReference.
Allele vcRef = vc.getReference(); Allele vcRef = vc.getReference();
if(!vcRef.basesMatch(hapRefValue)) { if(!vcRef.basesMatch(hapRefValue)) {
//TODO check the intersection of vcRef and hapRefValue
continue; //skip record continue; //skip record
} }
} }