vector<string> setParameters();
string getCommandName() { return "sort.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getHelpString();
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; }
- string getDescription() { return "puts sequences from a fasta, name, group, quality or taxonomy file in the same order"; }
+ string getDescription() { return "puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
map<string, int> names;
- string accnosfile, fastafile, namefile, groupfile, taxfile, qualfile, outputDir;
+ string accnosfile, fastafile, namefile, groupfile, taxfile, qualfile, flowfile, outputDir;
bool abort, large;
vector<string> outputNames;
int readFasta();
+ int readFlow();
int readName();
int readGroup();
- int readAccnos();
int readTax();
int readQual();