#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
+#include "qualityscores.h"
+#include "groupmap.h"
class TrimSeqsCommand : public Command {
public:
TrimSeqsCommand(string);
+ TrimSeqsCommand();
~TrimSeqsCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
-
+
+ GroupMap* groupMap;
+
struct linePair {
unsigned long int start;
- int num;
- linePair(unsigned long int i, int j) : start(i), num(j) {}
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
- void getOligos(vector<string>&);
- bool stripQualThreshold(Sequence&, ifstream&);
- bool cullQualAverage(Sequence&, ifstream&);
- int stripBarcode(Sequence&, int&);
- int stripForward(Sequence&, int&);
- 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);//, int, int&, int);
+ int countDiffs(string, string);
+ 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, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+ 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;
+ map<string, int> groupToIndex;
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 setLines(string, vector<linePair*>&);
+ 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, string, vector<unsigned long int>&, vector<unsigned long int>&);
};