pat's changes to trim.seqs

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 926326beb876087f1361278a9523759ab4bc3372..c2d9c45cfa931e9510981a4ff0c82c1d1e0fa890 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -28,9 +28,9 @@ public:
 private:
 
        struct linePair {
-               int start;
+               unsigned long int start;
                int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(j) {}
+               linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
@@ -42,12 +42,14 @@ private:
        int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
        #endif
 
-       bool abort, realign, MPIWroteAccnos;
+       bool abort, realign;
        string fastafile, templatefile, outputDir, search;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;
        
+       vector<string> outputNames;
+       vector<string> fastaFileNames;
        
 };