main(int argc, char* argv[])
{
SeqStructPtr seqP;
int count;
if (argc != 2)
{
fprintf(stderr,"Usage: %s <fasta format sequence file name>\n", argv[0]);
exit(1);
}
openFile(argv[1]);
initBuffer();
count = 0;
while (! endOfFile)
if (seqP = getSeq(argv[1]))
{
#ifdef DEBUG_SPUTNIK
fprintf(stdout,"processing sequence %d\n", count++);
#endif
/* dumpSeq(seqP); */
findRepeats(seqP);
free((void *)seqP);
}
}
static
bool requiresDedupe(const NGHolder &h, const flat_set<ReportID> &reports,
const Grey &grey) {
/* TODO: tighten */
NFAVertex seen_vert = NGHolder::null_vertex();
for (auto v : inv_adjacent_vertices_range(h.accept, h)) {
if (has_intersection(h[v].reports, reports)) {
if (seen_vert != NGHolder::null_vertex()) {
return true;
}
seen_vert = v;
}
}
for (auto v : inv_adjacent_vertices_range(h.acceptEod, h)) {
if (has_intersection(h[v].reports, reports)) {
if (seen_vert != NGHolder::null_vertex()) {
return true;
}
seen_vert = v;
}
}
if (seen_vert) {
/* if the reporting vertex is part of of a terminal repeat, the
* construction process may reform the graph splitting it into two
* vertices (pos, cyclic) and hence require dedupe */
vector<GraphRepeatInfo> repeats;
findRepeats(h, grey.minExtBoundedRepeatSize, &repeats);
for (const auto &repeat : repeats) {
if (find(repeat.vertices.begin(), repeat.vertices.end(),
seen_vert) != repeat.vertices.end()) {
return true;
}
}
}
return false;
}
