private double[] oneDprob(final EvidenceInterface evidence) {
final Code code = mSubHypotheses.code();
final double[] probs = new double[mSubHypotheses.size()];
for (int i = 0; i < probs.length; i++) {
final double a = Math.max(0, evidence.probability(code.a(i)));
final double b = Math.max(0, evidence.probability(code.bc(i)));
probs[i] = 0.5 * (a + b);
}
// System.err.println(probs.length + " :" + Arrays.toString(probs));
return probs;
}
/**
* @param diseaseHyp haploid disease hypothesis that starts with NONE and includes rest of
* nucleotides (see <code>HypothesesDisease</code>).
* @param genome selects family member with father starting at 0.
* @return true iff the disease hypothesis is consistent with the disease status of this family
* member (aka genome). Assumes disease is dominant.
*/
private boolean q(final int diseaseHyp, final int genome) {
final int hyp = mCurrentHypotheses[genome];
final boolean contains;
final Code code = mIndividualHypotheses.code();
final int dis = diseaseHyp - 1;
// TODO implement recessive version controlled by flag.
if (code.homozygous(hyp)) {
contains = code.a(hyp) == dis;
} else {
contains = code.a(hyp) == dis || code.b(hyp) == dis;
}
return contains == mFamily.isDiseased(genome);
}
@Override
public void increment(final EvidenceInterface evidence) {
// System.err.println(evidence);
incrementStatistics(evidence);
if (ambiguityShortCircuit(evidence)) {
return;
}
final double r = evidence.mapError();
final double rc = 1.0 - r;
// Avoid case where mapq is 0 which gives a NaN
if (rc <= 0.0) {
return;
}
final double[] probs = oneDprob(evidence);
final double pE = evidence.pe();
final double pEr = r * pE;
final Code code = hypotheses().code();
for (int i = 0; i < size(); i++) {
final int a = code.a(i);
final int b = code.bc(i);
// The cross-product is normal x cancer
final double prob = probs[a] * mContamination + probs[b] * mContaminationM;
// Phred scores of 0 can result in 0 probability, just skip them
if (prob <= 0.0) {
return;
}
// Adjust for mapQ - see theory in scoring.tex
final double pr = prob * rc + pEr;
final double np = arithmetic().multiply(mPosteriors[i], arithmetic().prob2Poss(pr));
assert arithmetic()
.isValidPoss(
np); // : System.err.println("np=" + np + " mPosteriors[i]=" + mPosteriors[i] + " i="
// + i + " pr=" + pr + " prob=" + prob + " rc=" + rc + " r=" + r + " pE=" + pE);
mPosteriors[i] = np;
}
}