pcr.seqs bug fix. working on shannon range calc

[mothur.git] / sracommand.h

diff --git a/sracommand.h b/sracommand.h
index 0f0a945d6118ad7ed17c4f08c7e2dce1dfa45bb0..3f7f1560530f8a8903db79b7a6f98b474ce50102 100644 (file)
--- a/sracommand.h
+++ b/sracommand.h
@@ -34,9 +34,15 @@ public:
     void help() { m->mothurOut(getHelpString()); }
     
 private:
-    bool abort;
-    string sfffiles, fastqfiles, platform, outputDir;
+    bool abort, isSFF;
+    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>&);
+    
 };
 
 /**************************************************************************************************/