//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
//check for required parameters
ct = new CountTable();
ct->readTable(countfile);
read->read(ct);
- }
+ }else { read->read(nameMap); }
list = read->getListVector();
matrix = read->getDMatrix();
loops = 0;
start = time(NULL);
+ oldRAbund.setLabel(label);
if (countfile == "") {
oldRAbund.print(rabundFile);
oldRAbund.getSAbundVector().print(sabundFile);
}
-
- oldRAbund.setLabel(label);
+
if (m->isTrue(showabund)) {
oldRAbund.getSAbundVector().print(cout);
}