#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
+#include "referencedb.h"
struct Compare {
int AA, AT, AG, AC, TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+ string getDescription() { return "seq.error"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
+ ReferenceDB* rdb;
struct linePair {
unsigned long int start;
string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
double threshold;
- bool ignoreChimeras, filter;
+ bool ignoreChimeras, save;
int numRefs, processors;
int maxLength, totalBases, totalMatches;
//ofstream errorSummaryFile, errorSeqFile;