Merge remote-tracking branch 'mothur/master'

[mothur.git] / makecontigscommand.h

diff --git a/makecontigscommand.h b/makecontigscommand.h
index 86a8450afaf76ba3be6a167ce8b856a605f09166..3300f692df857ca66d28a22501e63b848daa7625 100644 (file)
--- a/makecontigscommand.h
+++ b/makecontigscommand.h
@@ -49,8 +49,9 @@ public:
     string getCommandName()                    { return "make.contigs";                        }
     string getCommandCategory()                { return "Sequence Processing";         } 
     //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
-    string getOutputFileNameTag(string, string);
+    
        string getHelpString(); 
+    string getOutputPattern(string);   
     string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
     string getDescription()            { return "description"; }
     
@@ -59,7 +60,7 @@ public:
     
 private:
     bool abort, allFiles, createGroup;
-    string outputDir, ffastqfile, rfastqfile, align, oligosfile;
+    string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file;
        float match, misMatch, gapOpen, gapExtend;
        int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
     vector<string> outputNames;
@@ -78,7 +79,7 @@ private:
     //vector<string> groupVector;
     
     fastqRead readFastq(ifstream&, bool&);
-    vector< vector<string> > readFastqFiles(int&);
+    vector< vector<string> > readFastqFiles(unsigned long int&);
     bool checkReads(fastqRead&, fastqRead&);
     int createProcesses(vector< vector<string> >, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
     int driver(vector<string>, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);