~node_t()
{
child_iterator_range c_range(children.begin(), children.end());
for(child_iterator it = c_range.begin(); it != c_range.end(); ++it)
{
node_descriptor c = *it;
delete static_cast< node_t* >(c);
}
}
// Assumes children is empty
void copy_children_from(const node_t& rhs)
{
child_iterator_range c_range(rhs.children.begin(), rhs.children.end());
for(child_iterator it = c_range.begin(); it != c_range.end(); ++it)
{
node_descriptor c = *it;
children.push_back(copy_node(c));
static_cast< node_t* >(children.back())->parent = this;
}
}
void PE_match()
{
//find all matched paired end reads for every paired end read
//brute force
//clustering
long i, j, overlap_start, overlap_end;
PE_matchset_acknowledge_initialization();
for (i = 1; i < PE_num; i++)
{
//PE_matchset_acknowledge(PE_list_ordered[i], 50, 50, NULL);
PE_matchset_acknowledge(i, 50, 50, NULL);
j = i + 1;
cluster c_range(PE_list[PE_list_ordered[i]]);
while (j <= PE_num && PE_list[PE_list_ordered[j]]->startrange_low <= c_range.end1_range_high)// && PE_list[PE_list_ordered[j]]->endrange_low <= c_range.end2_range_high)
{
if (c_range.searchANDmodify(PE_list[PE_list_ordered[j]], &overlap_start, &overlap_end) == true)
{
//PE_matchset_acknowledge(PE_list_ordered[j], overlap_start, overlap_end, NULL);
PE_matchset_acknowledge(j, overlap_start, overlap_end, NULL);
}
j++;
}
PE_matchset_acknowledge(0, 0, 0, &c_range); //end the current set
}
PE_matchset_acknowledge_end();
return;
}