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When matching eval to comps, try to choose the one with the same alt allele.

This commit is contained in:
Eric Banks 2011-08-11 13:55:01 -04:00
parent 200f73b008
commit 90771b74b4
2 changed files with 18 additions and 8 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
View File

@ -39,7 +39,6 @@ import java.util.List;
* this class contains static helper methods for DbSNP
*/
public class DbSNPHelper {
public static final String STANDARD_DBSNP_TRACK_NAME = "dbsnp";
private DbSNPHelper() {} // don't make a DbSNPHelper

25
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -7,9 +7,7 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.Reference;
@ -22,11 +20,11 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -148,7 +146,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
// Add a dummy comp track if none exists
if ( comps.size() == 0 ) {
comps.add(new RodBinding(VariantContext.class, "none", "UNBOUND", "", new Tags()));
comps.add(new RodBinding<VariantContext>(VariantContext.class, "none", "UNBOUND", "", new Tags()));
}
// Cache the rod names
@ -329,14 +327,27 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
if ( eval == null )
return comps.iterator().next();
// find a matching comp
// find all of the matching comps
List<VariantContext> matchingComps = new ArrayList<VariantContext>(comps.size());
for ( VariantContext comp : comps ) {
if ( comp.getType() == eval.getType() )
return comp;
matchingComps.add(comp);
}
// if no matching comp, return null
return null;
if ( matchingComps.size() == 0 )
return null;
// find the comp which matches the alternate allele from eval
Allele altEval = eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
for ( VariantContext comp : matchingComps ) {
Allele altComp = comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
if ( (altEval == null && altComp == null) || (altEval != null && altEval.equals(altComp)) )
return comp;
}
// if none match, just return the first one
return matchingComps.get(0);
}
public Integer treeReduce(Integer lhs, Integer rhs) { return null; }