map<string, string> nameMap;
map<string, string>::iterator itNames;
if (oldNameMapFName != "") {
- m->readNames(oldNameMapFName, nameMap);
- if (oldNameMapFName == outNameFile){
- variables["[tag]"] = "unique";
- outNameFile = getOutputFileName("name", variables); }
+ m->readNames(oldNameMapFName, nameMap);
+ if (oldNameMapFName == outNameFile){
+ //prepare filenames and open files
+ map<string, string> mvariables;
+ mvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+ mvariables["[tag]"] = "unique";
+ outNameFile = getOutputFileName("name", mvariables);
+ }
}
CountTable ct;
if (countfile != "") {
- 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); }
}
if (m->control_pressed) { return 0; }
m->gobble(in);
- if(count % 1000 == 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }
+ if(count % 1000 == 0) { m->mothurOutJustToScreen(toString(count) + "\t" + toString(sequenceStrings.size()) + "\n"); }
}
if(count % 1000 != 0) { m->mothurOut(toString(count) + "\t" + toString(sequenceStrings.size())); m->mothurOutEndLine(); }