vector<string> setParameters();
string getCommandName() { return "remove.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+ string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
bool abort, dups;
vector<string> outputNames;
+ map<string, string> uniqueMap;
int readFasta();
+ int readFastq();
int readName();
int readGroup();
+ int readCount();
int readAlign();
int readList();
int readTax();