string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
- string getOutputPattern(string);
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
string getDescription() { return "trim sequence length"; }
linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
- string fastafile, outputDir, keep;
+ string fastafile, outputDir, keep, namefile, groupfile, countfile;
bool abort, countGaps, Short;
int numbases, processors;
vector<string> outputNames;