#include "countseqscommand.h"
#include "groupmap.h"
#include "sharedutilities.h"
+#include "counttable.h"
//**********************************************************************************************************************
vector<string> CountSeqsCommand::setParameters(){
string CountSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count.table file. You may also provide a group file to get the counts broken down by group.\n";
+ helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count_table file. You may also provide a group file to get the counts broken down by group.\n";
helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
it = outputTypes.find(type);
if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
else {
- if (type == "counttable") { outputFileName = "count.table"; }
+ if (type == "counttable") { outputFileName = "count_table"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
}
return outputFileName;
int total = 0;
if (!large) { total = processSmall(outputFileName); }
else { total = processLarge(outputFileName); }
-
+
if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
//set rabund file as new current rabundfile