ofstream out;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastaFile); }
- string outFastaFile = thisOutputDir + m->getRootName(m->getSimpleName(fastaFile));
- int pos = outFastaFile.find("unique");
- if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); }
- else { outFastaFile = outputDir + outFastaFile; }
- map<string, string> variables;
+ string outFastaFile = thisOutputDir + m->getRootName(m->getSimpleName(fastaFile));
+
+ map<string, string> variables;
variables["[filename]"] = outFastaFile;
outFastaFile = getOutputFileName("fasta", variables);
m->openOutputFile(outFastaFile, out);