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Using a VCF whose ALT is the reference in GGA mode is a User Error

This commit is contained in:
Eric Banks 2012-04-24 11:08:37 -04:00
parent 74ad008163
commit 91bad244d5
1 changed files with 8 additions and 2 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -36,6 +36,7 @@ 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.codecs.vcf.VCFConstants;
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;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
@ -67,11 +68,12 @@ 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);
final Allele refAllele = Allele.create(refBase, true);
// start making the VariantContext // start making the VariantContext
final GenomeLoc loc = ref.getLocus(); final GenomeLoc loc = ref.getLocus();
final List<Allele> alleles = new ArrayList<Allele>(); final List<Allele> alleles = new ArrayList<Allele>();
alleles.add(Allele.create(refBase, true)); alleles.add(refAllele);
final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), loc.getStop(), alleles); final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), loc.getStop(), alleles);
// calculate the GLs // calculate the GLs
@ -97,7 +99,11 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
// ignore places where we don't have a SNP // ignore places where we don't have a SNP
if ( vc == null || !vc.isSNP() ) if ( vc == null || !vc.isSNP() )
return null; return null;
// make sure a user isn't passing the REF base in as an ALT
if ( vc.hasAlternateAllele(refAllele, true) )
throw new UserException.BadInput("Alternate allele '" + (char)refBase + "' passed in is the same as the reference at location " + vc.getChr() + ":" + vc.getStart());
alleles.addAll(vc.getAlternateAlleles()); alleles.addAll(vc.getAlternateAlleles());
} else { } else {