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;
//delete inFileName;
if (pid == 0) {
- positions = setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+ positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
#else
ifstream in;
- openInputFile(file, in);
+ m->openInputFile(file, in);
//read in seqs and store in vector
while(!in.eof()){
if (m->control_pressed) { return container; }
- Sequence* current = new Sequence(in); gobble(in);
+ Sequence* current = new Sequence(in); m->gobble(in);
if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
else if (length != current->getAligned().length()) { unaligned = true; }
#else
ifstream infile;
- openInputFile(filename, infile);
+ m->openInputFile(filename, infile);
if (!infile.eof()) {
Sequence temp(infile);