string PrimerDesignCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The primer.design allows you to design sequence fragments that are specific to particular OTUs.\n";
+ helpString += "The primer.design allows you to identify sequence fragments that are specific to particular OTUs.\n";
helpString += "The primer.design command parameters are: list, fasta, name, count, otunumber, cutoff, length, pdiffs, mintm, maxtm, processors and label.\n";
helpString += "The list parameter allows you to provide a list file and is required.\n";
helpString += "The fasta parameter allows you to provide a fasta file and is required.\n";
#else
- counts = driverGetCounts(nameMap, fastaCount, otuCounts, 0, 1000);
+ unsigned long long start = 0;
+ unsigned long long end = 1000;
+ counts = driverGetCounts(nameMap, fastaCount, otuCounts, start, end);
#endif
//you will have a nameMap error if there is a namefile or countfile, but if those aren't given we want to make sure the fasta and list file match.
map<string, int> nameMap;
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, false);
vector<string> namesOfSeqs = ct.getNamesOfSeqs();
numSeqs = ct.getNumUniqueSeqs();