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;