string Maligner::getResults(Sequence* q) {
try {
+ outputResults.clear();
+
//make copy so trimming doesn't destroy query from calling class - remember to deallocate
query = new Sequence(q->getName(), q->getAligned());
//find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
refSeqs = decalc->findClosest(query, db, numWanted);
-
- ofstream out;
- string outFile = "parentsOf" + query->getName();
- openOutputFile(outFile, out);
- for (int i = 0; i < refSeqs.size(); i++) { refSeqs[i]->printSequence(out); }
- out.close();
-
+
refSeqs = minCoverageFilter(refSeqs);
if (refSeqs.size() < 2) {