/**
* Remove redundant entries such as duplicates and substrings e.g.
* {T,TT,TT} -> {TT}
* {A,C,CG,CGC} -> {A,CGC}
*/
void gpath_subset_rmsubstr(GPathSubset *subset)
{
if(subset->list.len <= 1) return;
if(!subset->is_sorted) gpath_subset_sort(subset);
size_t i, j, len = subset->list.len, min_juncs, ncols = subset->gpset->ncols;
GPath **list = subset->list.b;
// Work backwards to remove colours from subsumed paths
for(i = len-1; i > 0; i--) {
if(list[i] != NULL) {
// work backwards over paths as j as they match
for(j = i-1; j != SIZE_MAX; j--)
{
if(list[j] != NULL)
{
min_juncs = MIN2(list[i]->num_juncs, list[j]->num_juncs);
// j can't be a subset of i if it's longer,
// or orientations don't match
if(list[i]->num_juncs < list[j]->num_juncs ||
list[i]->orient != list[j]->orient ||
binary_seqs_cmp(list[i]->seq, min_juncs,
list[j]->seq, min_juncs) != 0)
{
break;
}
else if(list[i]->num_juncs == list[j]->num_juncs)
{
// paths match, steal colours from j and remove it
gpath_colset_or_mt(list[i], list[j], ncols);
gpath_set_nseen_sum_mt(list[i], subset->gpset,
list[j], subset->gpset);
list[j] = NULL;
}
else
{
// path j is substring of i, remove colours from j that are in i
// then remove path j only if all colours removed
if(gpath_colset_rm_intersect(list[i], list[j], ncols) == 0)
list[j] = NULL;
}
}
}
}
}
// loop over entries and remove empty ones
for(i = j = 0; i < len; i++)
if(list[i] != NULL)
list[j++] = list[i];
subset->list.len = j;
}
// Compare by orient, sequence
int gpath_cmp(const GPath *a, const GPath *b)
{
int ret = (int)a->orient - (int)b->orient;
return ret ? ret : binary_seqs_cmp(a->seq, a->num_juncs, b->seq, b->num_juncs);
}
