public void writeHapMap(ReadsByTaxa rbt, String outfileS, float coverRate) {
String[] hapMap;
ArrayList<String> al = new ArrayList();
for (int i = 0; i < cls.length; i++) {
String temp;
if (cls[i].ifSnp) {
temp = getHapMapRecord(rbt, i + 1, cls[i].queryIndex, cls[i].hitIndex, coverRate);
if (temp != null) {
al.add(temp);
}
}
}
hapMap = al.toArray(new String[al.size()]);
try {
BufferedWriter bw = new BufferedWriter(new FileWriter(outfileS), 65536);
bw.write("rs alleles chrom pos strand assembly center protLSID assayLSID panelLSID QCcode ");
for (int i = 0; i < rbt.getTaxaCount() - 1; i++) {
bw.write(rbt.getTaxaNames()[i] + "\t");
}
bw.write(rbt.getTaxaNames()[rbt.getTaxaCount() - 1]);
bw.newLine();
for (int i = 0; i < hapMap.length; i++) {
bw.write(hapMap[i]);
bw.newLine();
}
bw.flush();
bw.close();
} catch (Exception e) {
System.out.println(e.toString());
}
}
@Override
public DataSet performFunction(DataSet input) {
createMergeOutfile(infiles, outfilename);
fillMergeOutfile(infiles, outfilename);
if (hapmapFile != null) {
myLogger.info("Calling SNPs in good reads.");
ReadsByTaxa rbt = new ReadsByTaxa();
rbt.readTBTFile(new File(outfilename));
Clusters cls = new Clusters(rbt);
cls
.networkFilter(); // Really powerful, which generates 85% single locus SNPs in 282 maize
// lines
cls.alleleFrequencyFileter(
rbt,
(double) 0.20,
(double) 0.30); // Only for linkage pop which has allele frequency peaks
cls.heteozygoteFilter(rbt); // Seems not useful, need to be refined or removed
cls.writeHapMap(rbt, hapmapFile.getAbsolutePath(), (float) 0.9);
}
return null;
}