working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index a54b24f4471e5d7aab5c185952f65f500d6cec7a..b37d4c04ac397fb2ede7ba1d2e0501b9508e5b9d 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -36,9 +36,9 @@ 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
@@ -51,7 +51,7 @@ private:
        map<string, int> sortFastaFile(string, string);
                
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
        bool abort, realign, trim, trimera, save;
@@ -81,8 +81,8 @@ typedef struct slayerData {
        string blastlocation;
        bool trimera;
        bool trim, realign;
-       unsigned long int start;
-       unsigned long int end;
+       unsigned long long start;
+       unsigned long long end;
        int ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted;
        MothurOut* m;
        float divR;
@@ -92,7 +92,7 @@ typedef struct slayerData {
        int threadId;
        
        slayerData(){}
-       slayerData(string o, string fa, string ac, string f, string te, string se, string bl, bool tri, bool trm, bool re, MothurOut* mout, unsigned long int st, unsigned long int en, int ks, int ma, int mis, int win, int minS, int minC, int miBS, int minSN, int par, int it, int inc, int numw, float div, map<string, int> prior, int tid) {
+       slayerData(string o, string fa, string ac, string f, string te, string se, string bl, bool tri, bool trm, bool re, MothurOut* mout, unsigned long long st, unsigned long long en, int ks, int ma, int mis, int win, int minS, int minC, int miBS, int minSN, int par, int it, int inc, int numw, float div, map<string, int> prior, int tid) {
                outputFName = o;
                fasta = fa;
                accnos = ac;