#include "command.hpp"
#include "trimoligos.h"
+#include "oligos.h"
/**************************************************************************************************/
bool abort, isSFF, pairedOligos;
int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
string sfffile, fastqfile, outputDir, file, oligosfile, contactfile, inputfile, mimarksfile;
- string libStrategy, libSource, libSelection, libLayout, platform, instrumentModel, fileType, dataType;
+ string libStrategy, libSource, libSelection, libLayout, platform, instrumentModel, fileType, dataType, checkorient;
string submissionName, lastName, firstName, email, centerName, centerType, description, website, orientation, packageType;
- string projectName, grantId, grantTitle, grantAgency, projectTitle;
+ string projectName, grantId, grantTitle, grantAgency, projectTitle, inputDir;
vector<string> outputNames, Groups;
- vector<string> primerNameVector;
- vector<string> barcodeNameVector;
- map<string, string> Group2Barcode;
- map<string, string> Group2Primer;
+ map<string, vector<string> > Group2Barcode;
+ map<string, vector<string> > Group2Primer;
map<string, string> Group2Organism;
map<string, map<string, string> > mimarks; //group -> <field -> valueForGroup> ex. F003D001 -> <lat_lon -> 42.282026 -83.733850>
+ set<string> uniqueNames;
bool checkCasesInstrumentModels(string&);
bool checkCasesPlatforms(string&);