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'); }
+ //cout << currQual.getName() << endl;
}
string origSeq = currSeq.getUnaligned();
tempNameFileNames,
lines[process],
qLines[process]);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
//pass groupCounts to parent
if(createGroup){
}else if(type == "SPACER"){
spacer.push_back(oligo);
}
- else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
+ else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
}
m->gobble(inOligos);
}