working on pam

[mothur.git] / chimeraccodecommand.h

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index 2bf7a70fd159a93fcc813c3236aed97a8c18c916..52bf07d01f6a411b870e119f82ef97f7b6f45cbd 100644 (file)
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -26,7 +26,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.ccode";               }
        string getCommandCategory()             { return "Sequence Processing"; }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
@@ -36,9 +38,9 @@ public:
                
 private:
        struct linePair {
-               unsigned long int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
@@ -47,10 +49,10 @@ private:
        int createProcesses(string, string, string);
        
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
-       bool abort, filter;
+       bool abort, filter, save;
        string fastafile, templatefile, outputDir, maskfile;
        int processors, window, numwanted, numSeqs, templateSeqsLength;
        Chimera* chimera;