headerLines.add(new VCFFilterHeaderLine(INSUFFICIENT_DATA_FILTER_NAME, "The phase of the child's genotype cannot be determined (ie someone is a no-call)"));
headerLines.add(new VCFFilterHeaderLine(MENDELIAN_VIOLATION_FILTER_NAME, "No combination of the parents' alleles can yield the child's genotype (ie a possible Mendelian violation)"));
headerLines.add(new VCFInfoHeaderLine(TRANSMISSION_PROBABILITY_TAG_NAME, 1, VCFHeaderLineType.Float, "Probability that the phase is correct given that the genotypes are correct"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
}
<BUG>private int genotypeToIndex(Genotype g) {
if (g.isHomRef()) {
return 0;
} else if (g.isHet()) {
return 1;
}
return 2;
}</BUG>
private double computeTransmissionLikelihoodOfGenotypeConfiguration(Genotype mom, Genotype dad, Genotype child) {

headerLines.add(new VCFFilterHeaderLine(INSUFFICIENT_DATA_FILTER_NAME, "The phase of the child's genotype cannot be determined (ie someone is a no-call)"));
headerLines.add(new VCFFilterHeaderLine(MENDELIAN_VIOLATION_FILTER_NAME, "No combination of the parents' alleles can yield the child's genotype (ie a possible Mendelian violation)"));
headerLines.add(new VCFInfoHeaderLine(TRANSMISSION_PROBABILITY_TAG_NAME, 1, VCFHeaderLineType.Float, "Probability that the phase is correct given that the genotypes are correct"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
