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Don't exception out in these VE modules if the VCF has records that aren't just SNPs or indels

This commit is contained in:
Eric Banks 2012-05-21 09:38:52 -04:00
parent 3af3834d50
commit 92d8aa3d4c
2 changed files with 6 additions and 4 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
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@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -113,7 +112,8 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
} }
break; break;
default: default:
throw new UserException.BadInput("Unexpected variant context type: " + eval); //throw new UserException.BadInput("Unexpected variant context type: " + eval);
break;
} }
return; return;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
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@ -35,7 +35,6 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -186,7 +185,8 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
case SYMBOLIC: case SYMBOLIC:
return Type.CNV; return Type.CNV;
default: default:
throw new UserException.BadInput("Unexpected variant context type: " + vc); //throw new UserException.BadInput("Unexpected variant context type: " + vc);
return null;
} }
} }
@ -211,6 +211,8 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
return; return;
final Type type = getType(eval); final Type type = getType(eval);
if ( type == null )
return;
TypeSampleMap titvTable = null; TypeSampleMap titvTable = null;