try {
Ld ld = var1.calculateLd(var2);
if (ld.getR2() >= rSquare) {</BUG>
excludeSNPs[t] = true;
<BUG>}
} catch (LdCalculatorException ex) {
Logger.getLogger(CalculateSimpleGeneticRiskScore.class.getName()).log(Level.SEVERE, null, ex);</BUG>
}
}
}

nrSNPs++;
for (int t = snp + 1; t < nrSNPsThisChr; t++) {
if (!excludeSNPs[t]) {
RiskEntry riskE2 = valueE2.get(t);
if (Math.abs(riskE2.getPos() - riskE.getPos()) <= windowSize[1]) {
GeneticVariant var2 = genotypeData.getSnpVariantByPos(riskE2.getChr(), riskE2.getPos());
if (calculateFastLd(var1, var2) >= rSquare) {
excludeSNPs[t] = true;
