helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n";
helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n";
helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
selectedCount += validSecond.size();
//if the name in the first column is in the set then print it and any other names in second column also in set
selectedCount += validSecond.size();
//if the name in the first column is in the set then print it and any other names in second column also in set
//you want part of this row
if (validSecond.size() != 0) {
wroteSomething = true;
out << validSecond[0] << '\t';
//you want part of this row
if (validSecond.size() != 0) {
wroteSomething = true;
out << validSecond[0] << '\t';
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }