public static String convertGenotype(String genotype, String snp_id, CDataFrame snps) {
String major = snps.getStringValue(MAJOR, snp_id);
String minor = snps.getStringValue(MINOR, snp_id);
char allele1 = genotype.charAt(0);
char allele2 = genotype.charAt(1);
String str =
convertGenotype(allele1, major, minor) + SPACE + convertGenotype(allele2, major, minor);
// System.out.println("converted genotype "+genotype+" to "+str);
return str;
}
public static void writeDataFile(String filename, CDataFrame dataframe) {
String output = dataframe.toString();
output = PlinkHelper.stripMissingValueToken(output);
CFileHelper.writeFile(filename, output);
}