1.9

[mothur.git] / ccode.cpp

diff --git a/ccode.cpp b/ccode.cpp
index 56856a9e4ac545627068eec2786dfdb4c476d1fb..5fdf5d140fc731bdd714ed56923901a720fcdac9 100644 (file)
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -29,13 +29,15 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
        
        #ifdef USE_MPI
                
-               char inFileName[mapInfo.length()];
-               strcpy(inFileName, mapInfo.c_str());
+               char* inFileName = new char[mapInfo.length()];\r
+               memcpy(inFileName, mapInfo.c_str(), mapInfo.length());
                
                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 
                MPI_File_open(MPI_COMM_WORLD, inFileName, outMode, MPI_INFO_NULL, &outMap);  //comm, filename, mode, info, filepointer
                
+               delete inFileName;
+
                int pid;
                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
                
@@ -44,10 +46,11 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
                        
                        MPI_Status status;
                        int length = outString.length();
-                       char buf2[length];
-                       strcpy(buf2, outString.c_str()); 
+                       char* buf2 = new char[length];\r
+                       memcpy(buf2, outString.c_str(), length);
                                
                        MPI_File_write_shared(outMap, buf2, length, MPI_CHAR, &status);
+                       delete buf2;
                }
        #else
 
@@ -235,21 +238,23 @@ int Ccode::print(MPI_File& out, MPI_File& outAcc) {
                
                MPI_Status status;
                int length = outString.length();
-               char buf2[length];
-               strcpy(buf2, outString.c_str()); 
+               char* buf2 = new char[length];\r
+               memcpy(buf2, outString.c_str(), length);
                                
                MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
-                       
+               delete buf2;
+
                if (results) {
                        m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
                        outAccString += querySeq->getName() + "\n";
                        
                        MPI_Status statusAcc;
                        length = outAccString.length();
-                       char buf[length];
-                       strcpy(buf, outAccString.c_str()); 
+                       char* buf = new char[length];\r
+                       memcpy(buf, outAccString.c_str(), length);
                                
                        MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
+                       delete buf;
                }
 
                //free memory
@@ -267,10 +272,11 @@ int Ccode::printMapping(string& output) {
        try {
                        MPI_Status status;
                        int length = output.length();
-                       char buf[length];
-                       strcpy(buf, output.c_str()); 
+                       char* buf = new char[length];\r
+                       memcpy(buf, output.c_str(), length);
                                
                        MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status);
+                       delete buf;
 
        }
        catch(exception& e) {