X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makecontigscommand.h;fp=makecontigscommand.h;h=3300f692df857ca66d28a22501e63b848daa7625;hp=d641ec9b26065723ec91eabc70367017ac2f160d;hb=55bbd10379db27def51cec72a8819d775f73e45b;hpb=4542a79d20176ff0ee830b0f9d4f4c92637439d9

diff --git a/makecontigscommand.h b/makecontigscommand.h
index d641ec9..3300f69 100644
--- a/makecontigscommand.h
+++ b/makecontigscommand.h
@@ -60,7 +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;
@@ -79,7 +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> >);