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Adding option to VariantAnnotator to do strict allele matching when annotating with comp track concordance.

This commit is contained in:
Ryan Poplin 2011-12-18 15:27:23 -05:00
parent 953998dcd0
commit bc842ab3a5
2 changed files with 14 additions and 4 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -170,6 +170,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
@Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio") @Argument(fullName="MendelViolationGenotypeQualityThreshold",shortName="mvq",required=false,doc="The genotype quality treshold in order to annotate mendelian violation ratio")
public double minGenotypeQualityP = 0.0; public double minGenotypeQualityP = 0.0;
@Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp tracks that exactly match both reference and alternate alleles will be counted as concordant", required=false)
private boolean requireStrictAlleleMatch = false;
private VariantAnnotatorEngine engine; private VariantAnnotatorEngine engine;
private Collection<VariantContext> indelBufferContext; private Collection<VariantContext> indelBufferContext;
@ -211,6 +214,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
else else
engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit()); engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit());
engine.initializeExpressions(expressionsToUse); engine.initializeExpressions(expressionsToUse);
engine.setRequireStrictAlleleMatch(requireStrictAlleleMatch);
// setup the header fields // setup the header fields
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones

14
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -47,9 +47,11 @@ public class VariantAnnotatorEngine {
private List<GenotypeAnnotation> requestedGenotypeAnnotations; private List<GenotypeAnnotation> requestedGenotypeAnnotations;
private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>(); private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>();
private HashMap<RodBinding<VariantContext>, String> dbAnnotations = new HashMap<RodBinding<VariantContext>, String>(); private final HashMap<RodBinding<VariantContext>, String> dbAnnotations = new HashMap<RodBinding<VariantContext>, String>();
private AnnotatorCompatibleWalker walker; private final AnnotatorCompatibleWalker walker;
private GenomeAnalysisEngine toolkit; private final GenomeAnalysisEngine toolkit;
private boolean requireStrictAlleleMatch = false;
protected static class VAExpression { protected static class VAExpression {
@ -163,6 +165,10 @@ public class VariantAnnotatorEngine {
return descriptions; return descriptions;
} }
public void setRequireStrictAlleleMatch( final boolean requireStrictAlleleMatch ) {
this.requireStrictAlleleMatch = requireStrictAlleleMatch;
}
public VariantContext annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) { public VariantContext annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
Map<String, Object> infoAnnotations = new LinkedHashMap<String, Object>(vc.getAttributes()); Map<String, Object> infoAnnotations = new LinkedHashMap<String, Object>(vc.getAttributes());
@ -197,7 +203,7 @@ public class VariantAnnotatorEngine {
} else { } else {
boolean overlapsComp = false; boolean overlapsComp = false;
for ( VariantContext comp : tracker.getValues(dbSet.getKey(), ref.getLocus()) ) { for ( VariantContext comp : tracker.getValues(dbSet.getKey(), ref.getLocus()) ) {
if ( !comp.isFiltered() ) { if ( !comp.isFiltered() && ( !requireStrictAlleleMatch || comp.getAlleles().equals(vc.getAlleles()) ) ) {
overlapsComp = true; overlapsComp = true;
break; break;
} }