@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;
}
