#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;
unsigned long int end;
linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
-
- void getOligos(vector<string>&, vector<string>&);
+
+ void getOligos(vector<vector<string> >&, vector<vector<string> >&);
int stripBarcode(Sequence&, QualityScores&, int&);
int stripForward(Sequence&, QualityScores&, int&);
bool stripReverse(Sequence&, QualityScores&);
+
+ bool keepFirstTrim(Sequence&, QualityScores&);
+ bool removeLastTrim(Sequence&, QualityScores&);
+
bool cullLength(Sequence&);
bool cullHomoP(Sequence&);
bool cullAmbigs(Sequence&);
bool compareDNASeq(string, string);
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, processors, tdiffs, bdiffs, pdiffs, comboStarts;
- int qWindowSize, qWindowStep;
+ int qWindowSize, qWindowStep, keepFirst, removeLast;
double qRollAverage, qThreshold, qWindowAverage, qAverage;
vector<string> revPrimer, outputNames;
set<string> filesToRemove;
vector<string> groupVector;
map<string, int> primers;
map<string, int> combos;
-
+ map<string, int> groupToIndex;
+ vector<string> primerNameVector; //needed here?
+ vector<string> barcodeNameVector; //needed here?
+ vector<int> groupCounts; //same order as barcodeNameVector
+
vector<int> processIDS; //processid
vector<linePair*> lines;
vector<linePair*> qLines;
- 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 driverCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);
+ int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
-
};
#endif