#define Mothur_sracommand_h
#include "command.hpp"
-
+#include "trimoligos.h"
/**************************************************************************************************/
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, isSFF;
+ bool abort, isSFF, pairedOligos;
int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
- string sfffile, fastqfile, platform, outputDir, groupfile, file, oligosfile;
- vector<string> outputNames;
-
- int readFile(vector<string>&);
- int parseSffFile(vector<string>&);
- int parseFastqFile(vector<string>&);
+ string sfffile, fastqfile, outputDir, groupfile, file, oligosfile, contactfile, inputfile;
+ string libStrategy, libSource, libSelection, libLayout, platform, instrumentModel, fileType;
+ string submissionName, lastName, firstName, email, centerName, centerType, description;
+ vector<string> outputNames, Groups, revPrimer;
+ vector<string> primerNameVector;
+ vector<string> barcodeNameVector;
+ map<string, string> Group2Barcode;
+ map<int, oligosPair> pairedBarcodes;
+ map<int, oligosPair> pairedPrimers;
+ map<string, int> barcodes;
+ map<string, int> primers;
+ vector<string> linker;
+ vector<string> spacer;
+
+ bool checkCasesInstrumentModels(string&);
+ bool checkCasesPlatforms(string&);
+ bool checkCasesLibStrategy(string&);
+ bool checkCasesLibSource(string&);
+ bool checkCasesLibSelection(string&);
+ int readFile(map<string, vector<string> >&);
+ int readContactFile();
+ int readOligos();
+ int parseSffFile(map<string, vector<string> >&);
+ int parseFastqFile(map<string, vector<string> >&);
+ int checkGroups(map<string, vector<string> >&);
+ int mapGroupToFile(map<string, vector<string> >&, vector<string>);
+ string reverseOligo(string oligo);
};