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Fixing issue in VariantEval in which insertion and deletion events weren't treated symmetrically. Added new option to require strict allele matching.

This commit is contained in:
Ryan Poplin 2011-09-12 09:43:23 -04:00
parent 07d365ce39
commit 60ebe68aff
1 changed files with 8 additions and 5 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -55,7 +55,7 @@ import java.util.*;
*
* <h2>Output</h2>
* <p>
* Evaluation tables.
* Evaluation tables detailing the results of the eval modules which were applied.
* </p>
*
* <h2>Examples</h2>
@ -152,6 +152,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
@Argument(fullName="ancestralAlignments", shortName="aa", doc="Fasta file with ancestral alleles", required=false)
private File ancestralAlignmentsFile = null;
@Argument(fullName="requireStrictAlleleMatch", shortName="strict", doc="If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping", required=false)
private boolean requireStrictAlleleMatch = false;
// Variables
private Set<SortableJexlVCMatchExp> jexlExpressions = new TreeSet<SortableJexlVCMatchExp>();
@ -360,16 +363,16 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
if ( matchingComps.size() == 0 )
return null;
// find the comp which matches the alternate allele from eval
// find the comp which matches both the reference allele and 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)) )
if ( (altEval == null && altComp == null) || (altEval != null && altEval.equals(altComp) && eval.getReference().equals(comp.getReference())) )
return comp;
}
// if none match, just return the first one
return matchingComps.get(0);
// if none match, just return the first one unless we require a strict match
return (requireStrictAlleleMatch ? null : matchingComps.get(0));
}
public Integer treeReduce(Integer lhs, Integer rhs) { return null; }