/**
* Get genotype string by index
*
* <p>WARNING: If the genotype is missing, it returns an empty string. E.g.: './.' ->
* getGenotype(0) = ""
*
* @return
*/
public String getGenotype(int idx) {
parseFields(); // Lazy parse
if (genotype == null) return ""; // Missing genotype
int num = genotype[idx];
if (num < 0) return ""; // Missing genotype
return num == 0 ? vcfEntry.getRef() : vcfEntry.getAlts()[num - 1];
}
/**
* Parse GT field
*
* @param value
*/
void parseGt(String value) {
String gtStr[] = null;
if (value.indexOf('|') >= 0) {
gtStr = value.split("\\|");
phased = true; // Phased
} else {
gtStr = value.split("/");
phased = false; // Unphased
}
// Create fields
genotype = new int[gtStr.length];
for (int i = 0; i < genotype.length; i++)
if (gtStr[i].isEmpty() || gtStr[i].equals("."))
genotype[i] = -1; // Genotype '-1' means missing values
else {
genotype[i] = Gpr.parseIntSafe(gtStr[i]);
// Sanity check
if ((genotype[i] - 1) >= vcfEntry.getAlts().length) {
boolean plural = vcfEntry.getAlts().length > 1;
throw new RuntimeException(
"Error: Bad genotype field '"
+ value
+ "'. Genotype says '"
+ genotype[i]
+ "' but there "
+ (plural ? "are" : "is")
+ " only '"
+ vcfEntry.getAlts().length
+ "' allele"
+ (plural ? "s" : "")
+ " ('"
+ vcfEntry.getAltsStr()
+ "').");
}
}
}
/**
* Return genotypes as string (e.g. "A/C")
*
* @return
*/
public String getGenotypeStr() {
parseFields(); // Lazy parse
StringBuilder sb = new StringBuilder();
if (genotype != null) {
for (int i = 0; i < genotype.length; i++) {
int num = genotype[i];
String gen = ".";
if (num == 0) gen = vcfEntry.getRef();
else if (num > 0) gen = vcfEntry.getAlts()[num - 1];
sb.append(gen);
if (i < (genotype.length - 1)) {
if (isPhased()) sb.append("|");
else sb.append("/");
}
}
}
return sb.toString();
}
