/**
* Is this entry heterozygous?
*
* <p>Infer Hom/Her if there is only one sample in the file. Ohtherwise the field is null.
*/
public Boolean calcHetero() {
// No genotyping information? => Use number of ALT field
if (genotypeFieldsStr == null) return isMultiallelic();
Boolean isHetero = null;
// No genotype fields => Parse fields (we only parse them if there is only one GT field)
if (genotypeFields == null) {
// Are there more than two tabs? (i.e. more than one format field + one genotype field)
int countFields, fromIndex;
for (countFields = 0, fromIndex = 0;
(fromIndex >= 0) && (countFields < 1);
countFields++, fromIndex++) fromIndex = genotypeFieldsStr.indexOf('\t', fromIndex);
// OK only one genotype field => Parse it in order to extract h**o info.
if (countFields == 1) parseGenotypes();
}
// OK only one genotype field => calculate if it is heterozygous
if ((genotypeFields != null) && (genotypeFields.length == 1))
isHetero = getVcfGenotype(0).isHeterozygous();
return isHetero;
}
public List<VcfGenotype> getVcfGenotypes() {
if (vcfGenotypes == null) parseGenotypes();
return vcfGenotypes;
}
