decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
}
mothurOut("Finding window breaks... "); cout.flush();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
it = trimmed[i].begin();
decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
}
mothurOut("Finding window breaks... "); cout.flush();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
it = trimmed[i].begin();