#include "removeseqscommand.h"
#include "sequence.hpp"
#include "listvector.hpp"
+#include "counttable.h"
//**********************************************************************************************************************
vector<string> RemoveSeqsCommand::setParameters(){
else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
else if (type == "qfile") { outputFileName = "pick" + m->getExtension(inputName); }
else if (type == "alignreport") { outputFileName = "pick.align.report"; }
- else if (type == "count") { outputFileName = "pick.count.table"; }
+ else if (type == "count") { outputFileName = "pick.count_table"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
}
return outputFileName;
}
in.close();
out.close();
+
+ //check for groups that have been eliminated
+ CountTable ct;
+ if (ct.testGroups(outputFileName)) {
+ ct.readTable(outputFileName);
+ ct.printTable(outputFileName);
+ }
+
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);