m->openInputFile(fastaFileNames[s], inFASTA);
ofstream outFASTA;
- string degapFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+ string tempOutputDir = outputDir;
+ if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
+ string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
m->openOutputFile(degapFile, outFASTA);
while(!inFASTA.eof()){