#include "trimoligos.h"
#include "alignment.hpp"
#include "needlemanoverlap.hpp"
+#include "counttable.h"
class PcrSeqsCommand : public Command {
public:
vector<string> setParameters();
string getCommandName() { return "pcr.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
string getDescription() { return "pcr.seqs"; }
vector<linePair> lines;
bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
bool abort, keepprimer, keepdots;
- string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch;
+ string fastafile, oligosfile, taxfile, groupfile, namefile, countfile, ecolifile, outputDir, nomatch;
int start, end, processors, length;
vector<string> revPrimer, outputNames;
int readName(set<string>&);
int readGroup(set<string>);
int readTax(set<string>);
+ int readCount(set<string>);
bool readOligos();
bool readEcoli();
int driverPcr(string, string, string, set<string>&, linePair);
}
set<int> lengths;
- pDataArray->count = pDataArray->fend;
+
for(int i = 0; i < pDataArray->fend; i++){ //end is the number of sequences to process
-
+ pDataArray->count++;
if (pDataArray->m->control_pressed) { break; }
Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA);