56624a200ddc511a15026ab4a5ad42d4aab88b9f,GeneticRiskScoreCalculator/src/main/java/nl/systemsgenetics/simplegeneticriskscorecalculator/CalculateSimpleGeneticRiskScore.java,CalculateSimpleGeneticRiskScore,calculate,#RandomAccessGenotypeData#HashMap#File#number#number#boolean#,34

Before Change


        for (int counter = 0; counter < chrOrder.length; counter++) {
            for (Entry<String, LinkedHashMap<String, HashMap<String, ArrayList<RiskEntry>>>> riskScorePheno : risks.entrySet()) {
                HashSet<String> excludeList = new HashSet<String>();
                for (Entry<String, HashMap<String, ArrayList<RiskEntry>>> riskScorePheno2 : riskScorePheno.getValue().entrySet()) {
                    String NameOfEntry = riskScorePheno.getKey() + riskScorePheno2.getKey();
                    int rowNr = scores.getHashRows().get(NameOfEntry);
                    try {
                        TextFile out = null;
                        if (debugMode) {
                            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;

//                        System.out.println("Processing chromosome:\t" + chrOrder[counter]);
                        if (riskScorePheno2.getValue().containsKey(chrOrder[counter])) {

                            ArrayList<RiskEntry> valueE2 = riskScorePheno2.getValue().get(chrOrder[counter]);

                            int nrSNPsThisChr = valueE2.size();
                            boolean[] excludeSNPs = new boolean[nrSNPsThisChr];

After Change


//Here we need to change the loop.
                for (double pVal : pValueThreshold){
                    String key = "_P" + pVal;
                    THashMap<String, ArrayList<RiskEntry>> riskScorePheno2 = riskScorePheno.getValue().get(key);
                    String NameOfEntry = riskScorePheno.getKey() + key;
                    int rowNr = scores.getHashRows().get(NameOfEntry);
                    try {