#include "command.hpp"
#include "sequence.hpp"
#include "qualityscores.h"
+#include "groupmap.h"
class TrimSeqsCommand : public Command {
public:
void help();
private:
-
+
+ GroupMap* groupMap;
+
struct linePair {
unsigned long int start;
unsigned long int end;
map<string, vector<string> > outputTypes;
bool abort;
- string fastaFile, oligoFile, qFileName, outputDir;
+ string fastaFile, oligoFile, qFileName, groupfile, outputDir;
bool flip, allFiles, qtrim;
int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
vector<string> groupVector;
map<string, int> primers;
map<string, int> combos;
+ map<string, int> groupToIndex;
vector<int> processIDS; //processid
vector<linePair*> lines;