X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sracommand.h;h=5cc371447ecb0b47605c642eb523afe7d2d7bac6;hb=cac38e9e251998fa0b825d00189534534948d226;hp=0f0a945d6118ad7ed17c4f08c7e2dce1dfa45bb0;hpb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;p=mothur.git

diff --git a/sracommand.h b/sracommand.h
index 0f0a945..5cc3714 100644
--- a/sracommand.h
+++ b/sracommand.h
@@ -10,7 +10,7 @@
 #define Mothur_sracommand_h
 
 #include "command.hpp"
-
+#include "trimoligos.h"
 
 /**************************************************************************************************/
 
@@ -34,9 +34,36 @@ public:
     void help() { m->mothurOut(getHelpString()); }
     
 private:
-    bool abort;
-    string sfffiles, fastqfiles, platform, outputDir;
-    vector<string> outputNames;
+    bool abort, isSFF, pairedOligos;
+    int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
+    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);
+    
 };
 
 /**************************************************************************************************/