#include "command.hpp"
#include "sequence.hpp"
#include "referencedb.h"
+#include "counttable.h"
class SeqErrorCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "seq.error"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+ string getOutputPattern(string);
+ string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nhttp://www.mothur.org/wiki/Seq.error"; }
string getDescription() { return "seq.error"; }
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;
+ bool ignoreChimeras, save, aligned;
int numRefs, processors;
int maxLength, totalBases, totalMatches;
//ofstream errorSummaryFile, errorSeqFile;