- //flow.files = 9 character offset
- compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
+ //we want to rip off .files, and also .flow if its there
+ string fileroot = m->getRootName(m->getSimpleName(flowFilesFileName));
+ if (fileroot[fileroot.length()-1] == '.') { fileroot = fileroot.substr(0, fileroot.length()-1); } //rip off dot
+ string extension = m->getExtension(fileroot);
+ if (extension == ".flow") { fileroot = m->getRootName(fileroot); }
+ else { fileroot += "."; } //add back if needed
+
+ compositeFASTAFileName = thisoutputDir + fileroot + "shhh.fasta";