added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index d29744ba39ba1791e27c306c7fd09f950ac15c0f..918b4e5e9bf8aa4a16a1e0ba0716e09753a29cea 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -38,9 +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
@@ -50,10 +50,10 @@ private:
        int createProcesses(string, string);
                
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
-       bool abort, svg;
+       bool abort, svg, save;
        string fastafile, templatefile, namefile, outputDir;
        int processors, increment, ksize, numSeqs, templateSeqsLength;
        Chimera* chimera;