vector<string> setParameters();
string getCommandName() { return "align.check"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getHelpString();
+
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
+ string getDescription() { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<int> structMap;
- string mapfile, fastafile, outputDir, namefile;
+ string mapfile, fastafile, outputDir, namefile, countfile;
bool abort;
int seqLength, haderror;
vector<string> outputNames;