#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, vector<string> > Group2Barcode;
map<string, vector<string> > Group2Primer;
map<string, string> Group2Organism;