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 {