<BUG>if (riskScorePheno2.getValue().containsKey(chrOrder[counter])) {ArrayList<RiskEntry> valueE2 = riskScorePheno2.getValue().get(chrOrder[counter]);int nrSNPsThisChr = valueE2.size();</BUG><CONTEXT>System.out.println(NameOfEntry);out = new TextFile(outputFolder + File.separator + NameOfEntry + "Chr" + chrOrder[counter] + ".log", TextFile.W);out.write("SNPs used for GRS calculation:\n");}int nrSNPs = 0;<extra_id_0>boolean[] excludeSNPs = new boolean[nrSNPsThisChr];if (excludeList.size() > 0) {</CONTEXT>
if (riskScorePheno2.containsKey(chrOrder[counter])) {ArrayList<RiskEntry> valueE2 = riskScorePheno2.get(chrOrder[counter]);int nrSNPsThisChr = valueE2.size();