d534241f35505d757f39d482d45d3316d6dd944e,java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java,FisherStrand,annotate,#RefMetaDataTracker#ReferenceContext#Map#VariantContext#,54
Before Change
private static final double MIN_PVALUE = 1E-320;
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( ! vc.isVariant() || vc.isFiltered() || ! vc.isBiallelic() || ! vc.isSNP() )
return null;
int[][] table = getContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAllele(0));
After Change
int[][] table;
if (vc.isBiallelic() && vc.isSNP())
table = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAllele(0));
else if (vc.isIndel() || vc.isMixed()) {
table = getIndelContingencyTable(stratifiedContexts, vc);
if (table == null)
return null;
}
else
return null;