//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
-
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
m->openInputFile(fastafile, in);
string name;
- ofstream out;
- string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
- m->openOutputFile(newFastaName, out);
- int count = 1;
- string lastName = "";
+ //ofstream out;
+ //string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+ //m->openOutputFile(newFastaName, out);
+ //int count = 1;
+ //string lastName = "";
while(!in.eof()){
Sequence currSeq(in);
name = currSeq.getName();
- if (lastName == "") { lastName = name; }
- if (name != lastName) { count = 1; }
- lastName = name;
+ //if (lastName == "") { lastName = name; }
+ //if (name != lastName) { count = 1; }
+ // lastName = name;
- Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
- newSeq.printSequence(out);
+ //Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
+ //newSeq.printSequence(out);
if (name != "") { names.push_back(name); }
m->gobble(in);
- count++;
+ //count++;
}
in.close();
- out.close();
+ //out.close();
return 0;