bool GaussianEdgeCalculator::edgeBetween(const AlignmentRecord & ap1, const AlignmentRecord & ap2, int numGCAllowedPos, int ct) const {
if (ap1.isSingleEnd() || ap2.isSingleEnd()) {
throw runtime_error("Cannot process single-end reads in GaussianEdgeCalculator!");
}
double insert_length_diff = abs(((int)ap1.getInsertLength()) - ((int)ap2.getInsertLength()));
// double meanedge = 2.0 * sf( insert_length_diff / (sqrt2*insert_size_popstddev) );
if (insert_length_diff > allowable_insert_size_diff) {
return false;
}
size_t intersection_length = ap1.internalSegmentIntersectionLength(ap2);
if (intersection_length == 0) return false;
double mean_insert_length = (ap1.getInsertLength() + ap2.getInsertLength()) / 2.0;
double interedge = min(1.0, 2.0 * sf(sqrt2*(mean_insert_length - intersection_length - insert_size_popmean) / insert_size_popstddev) );
return interedge >= significance_level;
}
double QuasispeciesEdgeCalculator::computeOverlap(const AlignmentRecord & ap1, const AlignmentRecord & ap2, const double cutoff) const {
double MIN_OVERLAP = 0;
if (ap1.getName().find("Clique") != string::npos
&& ap2.getName().find("Clique") != string::npos) {
MIN_OVERLAP = MIN_OVERLAP_CLIQUES;
} else {
MIN_OVERLAP = MIN_OVERLAP_SINGLE;
}
if (ap1.isSingleEnd() && ap2.isSingleEnd()) {
int read_size1 = min(ap1.getEnd1() - ap1.getStart1(), ap2.getEnd1() - ap2.getStart1());
float overlap_size1 = overlapSize(ap1.getEnd1(), ap2.getEnd1(), ap1.getStart1(), ap2.getStart1());
if (MIN_OVERLAP <= 1) overlap_size1 /= (float) read_size1;
if (overlap_size1 < MIN_OVERLAP) return 0;
// if (!is_disjoint(ap1.getReadNames(),ap2.getReadNames())) return 1;
return singleOverlap(ap1, ap2, 1, 1, MIN_OVERLAP, cutoff);
} else if (ap1.isSingleEnd() || ap2.isSingleEnd()) {
if (ap1.isSingleEnd()) {
int read_size1 = min(ap1.getEnd1() - ap1.getStart1(), ap2.getEnd1() - ap2.getStart1());
int read_size2 = min(ap1.getEnd1() - ap1.getStart1(), ap2.getEnd2() - ap2.getStart2());
float overlap_size1 = overlapSize(ap1.getEnd1(), ap2.getEnd1(), ap1.getStart1(), ap2.getStart1());
float overlap_size2 = overlapSize(ap1.getEnd1(), ap2.getEnd2(), ap1.getStart1(), ap2.getStart2());
if (MIN_OVERLAP <= 1) {
overlap_size1 /= (float) read_size1;
overlap_size2 /= (float) read_size2;
}
if ((overlap_size1 >= MIN_OVERLAP && overlap_size2 >= MIN_OVERLAP) || (overlap_size1+overlap_size2 >= MIN_OVERLAP && overlap_size1 > 0 && overlap_size2 > 0)) {
// if (!is_disjoint(ap1.getReadNames(),ap2.getReadNames())) return 1;
return singleOverlap(ap1, ap2, 1, 1, MIN_OVERLAP, cutoff)*singleOverlap(ap1, ap2, 1, 2, MIN_OVERLAP, cutoff);
}
return 0;
} else {
int read_size1 = min(ap1.getEnd1() - ap1.getStart1(), ap2.getEnd1() - ap2.getStart1());
int read_size2 = min(ap1.getEnd2() - ap1.getStart2(), ap2.getEnd1() - ap2.getStart1());
float overlap_size1 = overlapSize(ap1.getEnd1(), ap2.getEnd1(), ap1.getStart1(), ap2.getStart1());
float overlap_size2 = overlapSize(ap1.getEnd2(), ap2.getEnd1(), ap1.getStart2(), ap2.getStart1());
if (MIN_OVERLAP <= 1) {
overlap_size1 /= (float) read_size1;
overlap_size2 /= (float) read_size2;
}
if ((overlap_size1 >= MIN_OVERLAP && overlap_size2 >= MIN_OVERLAP) || (overlap_size1+overlap_size2 >= MIN_OVERLAP && overlap_size1 > 0 && overlap_size2 > 0)) {
// if (!is_disjoint(ap1.getReadNames(),ap2.getReadNames())) return 1;
return singleOverlap(ap1, ap2, 1, 1, MIN_OVERLAP, cutoff)*singleOverlap(ap1, ap2, 2, 1, MIN_OVERLAP, cutoff);
}
return 0;
}
} else {
int read_size1 = min(ap1.getEnd1() - ap1.getStart1(), ap2.getEnd1() - ap2.getStart1());
float overlap_size1 = overlapSize(ap1.getEnd1(), ap2.getEnd1(), ap1.getStart1(), ap2.getStart1());
if (MIN_OVERLAP <= 1) overlap_size1 /= (float) read_size1;
if (overlap_size1 < MIN_OVERLAP) return 0;
int read_size2 = min(ap1.getEnd2() - ap1.getStart2(), ap2.getEnd2() - ap2.getStart2());
float overlap_size2 = overlapSize(ap1.getEnd2(), ap2.getEnd2(), ap1.getStart2(), ap2.getStart2());
if (MIN_OVERLAP <= 1) overlap_size2 /= (float) read_size2;
if (overlap_size2 < MIN_OVERLAP) return 0;
// if (!is_disjoint(ap1.getReadNames(),ap2.getReadNames())) return 1;
return singleOverlap(ap1, ap2, 1, 1, MIN_OVERLAP, cutoff)*singleOverlap(ap1, ap2, 2, 2, MIN_OVERLAP, cutoff);
}
return 0;
}
