if (m->control_pressed) { return filterString; }
string seqAligned = seqs[i]->getAligned();
+
+ if (seqAligned.length() != filterString.length()) { m->mothurOut(seqs[i]->getName() + " is not the same length as the template sequences. Aborting!\n"); exit(1); }
for (int j = 0; j < seqAligned.length(); j++) {
//if this spot is a gap
#ifdef USE_MPI
int pid, processors;
- vector<long> positions;
+ vector<unsigned long int> positions;
int numSeqs;
int tag = 2001;