public void scan() {
// in the future this may call other scanOnChr to split the effort up more
long tests = 0;
int bestSite = -1, countSig = 0;
double bestP = 2;
for (int i = 0; i < refAlignment.getSiteCount(); i += step) {
// if(i%10000==0) System.out.println("scanChromosome
// chr:"+refAlignment.getChr()+"+site:"+i+" with Chr:"+refAlignment.getChr()+"
// test:"+tests);
if (Math.abs(refAlignment.getPositionInLocus(i) - blockPosition) < blockWindow) continue;
OpenBitSet mj = refAlignment.getSiteBitsNoClone(i, 0);
OpenBitSet mn = refAlignment.getSiteBitsNoClone(i, 1);
if (mn.lastCalculatedCardinality() > 4) {
double p = TagCallerAgainstAnchorMT.testSites(obsymj, mj, mn, binomFunc);
if (p < bestP) {
bestP = p;
bestSite = i;
}
if (p < sigThreshold) {
countSig++;
if (minSigPos == -1) minSigPos = refAlignment.getPositionInLocus(i);
maxSigPos = refAlignment.getPositionInLocus(i);
}
}
tests++;
}
int chr = Integer.parseInt(refAlignment.getLocus(bestSite).getChromosomeName());
double[] result = {chr, bestSite, refAlignment.getPositionInLocus(bestSite), bestP, countSig};
// if(bestP<0.000001) System.out.println(Arrays.toString(result));
resultReport[resultIndex] = result;
}
public double testSiteSimple(OpenBitSet dA1, OpenBitSet dA2, OpenBitSet dT, OpenBitSet dF) {
double result = 1;
int cntIA1 = 0, cntIA2 = 0;
cntIA1 = (int) OpenBitSet.intersectionCount(dT, dA1);
cntIA2 = (int) OpenBitSet.intersectionCount(dT, dA2);
int sum = cntIA1 + cntIA2;
if (sum > 0) {
if (cntIA1 < cntIA2) result = (double) cntIA1 / sum;
else result = (double) cntIA2 / sum;
}
/*
if (result < 0.0001) {
int cA1 = (int)dA1.lastCalculatedCardinality();
int cA2 = (int)dA2.lastCalculatedCardinality();
int cT = (int)dT.lastCalculatedCardinality();
int cF = (int)dF.lastCalculatedCardinality();
int cntIA1F = (int)OpenBitSet.intersectionCount(dF, dA1);
int cntIA2F = (int)OpenBitSet.intersectionCount(dF, dA2);
System.out.println(cntIA1 + "\t" + cntIA2 + "\t" + sum +"\t"+cA1+"\t"+cA2+"\t"+cT+"\t"+cF+"\t"+cntIA1F+"\t"+cntIA2F);
}
*
*/
return result;
}
public boolean checkAnchorSegregationInFamilies(
OpenBitSet familiesMark, OpenBitSet dA1, OpenBitSet dA2, int familySize) {
int cntA1 = (int) OpenBitSet.intersectionCount(familiesMark, dA1);
int cntA2 = (int) OpenBitSet.intersectionCount(familiesMark, dA2);
if (cntA1 > cntA2) {
int temp = cntA1;
cntA1 = cntA2;
cntA2 = temp;
}
int sum = cntA1 + cntA2;
double rate = (double) cntA1 / sum;
if (rate < 0.2) return false; // check segregation
// if ((double)sum/familySize < 0.8) return false; //check missing data
return true;
}
public double testSiteBio(OpenBitSet dA1, OpenBitSet dA2, OpenBitSet dT, OpenBitSet dF) {
double result = 1, minorP = 1;
int cntIA1 = 0, cntIA2 = 0, cntIA1T = 0, cntIA2T = 0, cntIA1F = 0, cntIA2F = 0;
cntIA1T = (int) OpenBitSet.intersectionCount(dT, dA1);
cntIA2T = (int) OpenBitSet.intersectionCount(dT, dA2);
cntIA1F = (int) OpenBitSet.intersectionCount(dF, dA1);
cntIA2F = (int) OpenBitSet.intersectionCount(dF, dA2);
int sumTag = cntIA1T + cntIA2T;
if (sumTag == 0) return result;
int sumAnchor = cntIA1F + cntIA2F;
if (cntIA1T < cntIA2T) {
minorP = (double) cntIA1F / sumAnchor;
} else {
minorP = (double) cntIA2F / sumAnchor;
}
Binomial binomFunc = new Binomial(5, 0.5, new RandomJava());
binomFunc.setNandP(sumTag, minorP);
try {
result = (cntIA1T < cntIA2T) ? binomFunc.cdf(cntIA1T) : binomFunc.cdf(cntIA2T);
} catch (Exception e) {
System.out.println(e.toString());
}
return result;
}