string CountSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.seqs command reads a name file and outputs a .count.summary file. You may also provide a group file to get the counts broken down by group.\n";
+ helpString += "The count.seqs command reads a name file and outputs a .seq.count 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 += "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";
helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "count.summary";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + ".seq.count";
m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
out << "Representative Sequence\t total\t";