X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sracommand.h;h=7bf764b640534d11b5d40242d210bc77064a00de;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=0f0a945d6118ad7ed17c4f08c7e2dce1dfa45bb0;hpb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;p=mothur.git

diff --git a/sracommand.h b/sracommand.h
index 0f0a945..7bf764b 100644
--- a/sracommand.h
+++ b/sracommand.h
@@ -35,8 +35,14 @@ public:
     
 private:
     bool abort;
-    string sfffiles, fastqfiles, platform, outputDir;
+    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>&);
+    
 };
 
 /**************************************************************************************************/