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Handle NPE generated in UG when non-standard reference bases are present in the fasta

This commit is contained in:
Eric Banks 2012-07-18 15:16:27 -04:00
parent 9af2cfe283
commit 659eee13a6
1 changed files with 3 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -35,7 +35,6 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -43,7 +42,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
@ -68,9 +66,11 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
final byte refBase = ref.getBase(); final byte refBase = ref.getBase();
final int indexOfRefBase = BaseUtils.simpleBaseToBaseIndex(refBase); final int indexOfRefBase = BaseUtils.simpleBaseToBaseIndex(refBase);
// handle non-standard reference bases
if ( indexOfRefBase == -1 )
return null;
final Allele refAllele = Allele.create(refBase, true); final Allele refAllele = Allele.create(refBase, true);
// calculate the GLs // calculate the GLs
ArrayList<SampleGenotypeData> GLs = new ArrayList<SampleGenotypeData>(contexts.size()); ArrayList<SampleGenotypeData> GLs = new ArrayList<SampleGenotypeData>(contexts.size());
for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) { for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {