#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
+#include "qualityscores.h"
+#include "groupmap.h"
class TrimSeqsCommand : public Command {
public:
TrimSeqsCommand(string);
- ~TrimSeqsCommand();
- int execute();
- void help();
+ TrimSeqsCommand();
+ ~TrimSeqsCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "trim.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
-
+
+ GroupMap* groupMap;
+
struct linePair {
- int start;
- int num;
- linePair(long int i, int j) : start(i), num(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
+
+ 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&);
- void getOligos(vector<string>&);
- bool stripQualThreshold(Sequence&, ifstream&);
- bool cullQualAverage(Sequence&, ifstream&);
- int stripBarcode(Sequence&, int&);
- int stripForward(Sequence&, int&);
- bool stripReverse(Sequence&);
bool cullLength(Sequence&);
bool cullHomoP(Sequence&);
bool cullAmbigs(Sequence&);
bool compareDNASeq(string, string);
- int countDiffs(string, string);//, int, int&, int);
+ int countDiffs(string, string);
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, keepFirst, removeLast;
+ 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<string> primerNameVector; //needed here?
+ vector<string> barcodeNameVector; //needed here?
+ map<string, int> groupCounts;
+
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<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