modified trim.seqs to account for primers of different lengths

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 8042983911c1052e100133b4284f03ddce751031..b100287269f16781839c884bd83121c620e279ba 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -32,15 +32,20 @@ private:
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
+       bool MPIWroteAccnos;
        
        AlignmentDB* templateDB;
        Alignment* alignment;
        
        int driver(linePair*, string, string, string, string);
-       void createProcesses(string, string, string, string);
+       int createProcesses(string, string, string, string);
        void appendAlignFiles(string, string); 
        void appendReportFiles(string, string);
        
+       #ifdef USE_MPI
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+       #endif
+       
        string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
        float match, misMatch, gapOpen, gapExtend, threshold;
        int processors, kmerSize;