#include "command.hpp"
#include "sequence.hpp"
#include "referencedb.h"
+#include "counttable.h"
class SeqErrorCommand : public Command {
int driver(string, string, string, string, string, string, linePair, linePair, linePair);
int createProcesses(string, string, string, string, string, string);
- string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
+ string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir, countfile;
double threshold;
bool ignoreChimeras, save, aligned;
int numRefs, processors;