Sequence currSeq(inFASTA); m->gobble(inFASTA);
//cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
+ if (m->debug) { m->mothurOut("[DEBUG]: " + toString(count) + " fasta = " + currSeq.getName() + '\n'); }
QualityScores currQual;
if(qFileName != ""){
currQual = QualityScores(qFile); m->gobble(qFile);
+ if (m->debug) { m->mothurOut("[DEBUG]: qual = " + currQual.getName() + '\n'); }
}
string origSeq = currSeq.getUnaligned();
}
for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+ if (m->debug) { m->mothurOut("[DEBUG]: " + toString(i) +'\t' + toString(fastaFilePos[i]) + '\t' + toString(fastaFilePos[i+1]) + '\n'); }
lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)])); }
}