private int allele(BitSet bits, int bitsPerAllele, int sample) {
if (sample >= samples.nSamples()) {
throw new IndexOutOfBoundsException(String.valueOf(sample));
}
int start = bitsPerAllele * sample;
int end = start + bitsPerAllele;
int allele = 0;
int mask = 1;
for (int j = start; j < end; ++j) {
if (bits.get(j)) {
allele += mask;
}
mask <<= 1;
}
return allele;
}
@Override
public int nHapPairs() {
return samples.nSamples();
}
@Override
public int nHaps() {
return 2 * samples.nSamples();
}