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;
}
