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Bugfix for OneBPIndel 

-- Previously was only including 1 bp insertions in stratification
This commit is contained in:
Mark DePristo 2012-04-09 15:50:20 -04:00
parent 2aa2d9aec0
commit bfa966a4e9
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
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@ -50,7 +50,7 @@ public class OneBPIndel extends VariantStratifier {
public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
if (eval != null && eval.isIndel()) { if (eval != null && eval.isIndel()) {
for ( int l : eval.getIndelLengths() ) for ( int l : eval.getIndelLengths() )
if ( l > 1 ) if ( Math.abs(l) > 1 )
return TWO_PLUS_BP; // someone is too long return TWO_PLUS_BP; // someone is too long
return ONE_BP; // all lengths are one return ONE_BP; // all lengths are one
} else } else