#include "needlemanoverlap.hpp"
#include "blastalign.hpp"
#include "noalign.hpp"
-
+#include "trimoligos.h"
struct fastqRead {
vector<int> scores;
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort;
- string outputDir, ffastqfile, rfastqfile, align;
+ bool abort, allFiles;
+ string outputDir, ffastqfile, rfastqfile, align, oligosfile;
float match, misMatch, gapOpen, gapExtend;
- int processors, longestBase, threshold;
+ int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
vector<string> outputNames;
+ map<int, oligosPair> barcodes;
+ map<int, oligosPair> primers;
+ vector<string> linker;
+ vector<string> spacer;
+ vector<string> primerNameVector;
+ vector<string> barcodeNameVector;
+
+ map<string, int> groupCounts;
+ //map<string, int> combos;
+ //map<string, int> groupToIndex;
+ //vector<string> groupVector;
+
fastqRead readFastq(ifstream&);
vector< vector<string> > readFastqFiles(int&);
bool checkReads(fastqRead&, fastqRead&);
int createProcesses(vector< vector<string> >, string, string, string);
int driver(vector<string>, string, string, string);
+ bool getOligos(vector<vector<string> >&, vector<vector<string> >&);
+ string reverseOligo(string);
};
/**************************************************************************************************/