void GaussianEdgeCalculator::getPartnerLengthRange(const AlignmentRecord& ap, unsigned int *min, unsigned int *max) const {
if ((unsigned)allowable_insert_size_diff > ap.getInsertLength()) {
*min = 0;
} else {
*min = ap.getInsertLength() - allowable_insert_size_diff;
}
*max = ap.getInsertLength() + allowable_insert_size_diff;
}
void AnyDistributionEdgeCalculator::getPartnerLengthRange(const AlignmentRecord& ap, unsigned int *min, unsigned int *max) const {
if (allowable_insert_size_diff > (int)ap.getInsertLength()) {
*min = 0;
} else {
*min = ap.getInsertLength() - allowable_insert_size_diff;
}
*max = ap.getInsertLength() + allowable_insert_size_diff;
}
bool AnyDistributionEdgeCalculator::edgeBetween(const AlignmentRecord & ap1, const AlignmentRecord & ap2) const {
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.intersectionLength(ap2);
if (intersection_length == 0) return false;
int insert_length_sum = ap1.getInsertLength() + ap2.getInsertLength() - 2*intersection_length;
double intersection_pvalue = insertSizeSumRightTail(insert_length_sum);
return intersection_pvalue >= significance_level;
}
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;
}
