- ct.readTable(countfile);
- if (countfile == outCountFile){
- variables["[tag]"] = "unique";
- outCountFile = getOutputFileName("count", variables); }
+ ct.readTable(countfile, true, false);
+ if (countfile == outCountFile){
+ //prepare filenames and open files
+ map<string, string> mvariables;
+ mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+ mvariables["[tag]"] = "unique";
+ outCountFile = getOutputFileName("count", mvariables); }