#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
+#include "qualityscores.h"
class TrimSeqsCommand : public Command {
public:
private:
struct linePair {
- int start;
+ unsigned long int start;
int num;
- linePair(long int i, int j) : start(i), num(j) {}
+ linePair(unsigned long int i, int j) : start(i), num(j) {}
};
- void getOligos(vector<string>&);
- bool stripQualThreshold(Sequence&, ifstream&);
- bool cullQualAverage(Sequence&, ifstream&);
- bool stripBarcode(Sequence&, int&);
- bool stripForward(Sequence&);
- bool stripReverse(Sequence&);
+ void getOligos(vector<string>&, vector<string>&);
+ int stripBarcode(Sequence&, QualityScores&, int&);
+ int stripForward(Sequence&, QualityScores&, int&);
+ bool stripReverse(Sequence&, QualityScores&);
bool cullLength(Sequence&);
bool cullHomoP(Sequence&);
bool cullAmbigs(Sequence&);
bool compareDNASeq(string, string);
+ int countDiffs(string, string);
bool abort;
string fastaFile, oligoFile, qFileName, outputDir;
bool flip, allFiles, qtrim;
- int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors;
- vector<string> forPrimer, revPrimer, outputNames;
+ int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+ int qWindowSize, qWindowStep;
+ double qRollAverage, qThreshold, qWindowAverage, qAverage;
+ vector<string> revPrimer, outputNames;
+ set<string> filesToRemove;
map<string, int> barcodes;
vector<string> groupVector;
+ map<string, int> primers;
+ map<string, int> combos;
vector<int> processIDS; //processid
vector<linePair*> lines;
vector<linePair*> qLines;
- int driverCreateTrim(string, string, string, string, string, vector<string>, linePair*, linePair*);
- int createProcessesCreateTrim(string, string, string, string, string, vector<string>);
+ int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);
+ int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
int setLines(string, vector<linePair*>&);
};