1.9

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 84c3219822920e21bc20d89f2fdf6b4f58ead1f3..1122c242d35e4a5891e87ac3aeaaaced048a9a56 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -310,11 +310,12 @@ int Pintail::print(MPI_File& out, MPI_File& outAcc) {
                        
                        MPI_Status statusAcc;
                        int 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;
+
                        results = true;
                }
                outputString += "Observed\t";
@@ -329,10 +330,11 @@ int Pintail::print(MPI_File& out, MPI_File& outAcc) {
                
                MPI_Status status;
                int length = outputString.length();
-               char buf2[length];
-               strcpy(buf2, outputString.c_str()); 
+               char* buf2 = new char[length];\r
+               memcpy(buf2, outputString.c_str(), length);
                                
                MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
+               delete buf2;
                
                return results;
        }
@@ -424,17 +426,19 @@ vector<float> Pintail::readFreq() {
                MPI_File inMPI;
                MPI_Offset size;
                MPI_Status status;
-               
-               char inFileName[consfile.length()];
-               strcpy(inFileName, consfile.c_str());
+
+               char* inFileName = new char[consfile.length()];\r
+               memcpy(inFileName, consfile.c_str(), consfile.length());
 
                MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  
                MPI_File_get_size(inMPI, &size);
+               delete inFileName;
 
-               char buffer[size];
+               char* buffer = new char[size];
                MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 
                string tempBuf = buffer;
+               delete buffer;
 
                if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
                istringstream iss (tempBuf,istringstream::in);
@@ -621,18 +625,21 @@ vector< vector<float> > Pintail::readQuantiles() {
                MPI_Offset size;
                MPI_Status status;
                
-               char inFileName[quanfile.length()];
-               strcpy(inFileName, quanfile.c_str());
+               char* inFileName = new char[quanfile.length()];\r
+               memcpy(inFileName, quanfile.c_str(), quanfile.length());
 
                MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  
                MPI_File_get_size(inMPI, &size);
+               delete inFileName;
+
 
-               char buffer[size];
+               char* buffer = new char[size];
                MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 
                string tempBuf = buffer;
                if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
                istringstream iss (tempBuf,istringstream::in);
+               delete buffer;
                
                while(!iss.eof()) {
                        iss >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine; 
@@ -700,21 +707,24 @@ void Pintail::printQuanFile(string file, string outputString) {
                        MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 
                        int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
-                       
-                       char FileName[file.length()];
-                       strcpy(FileName, file.c_str());
+
+                       char* FileName = new char[file.length()];\r
+                       memcpy(FileName, file.c_str(), file.length());
                        
                        if (pid == 0) {
                                MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outQuan);  //comm, filename, mode, info, filepointer
                                
                                int length = outputString.length();
-                               char buf[length];
-                               strcpy(buf, outputString.c_str()); 
+                               char* buf = new char[length];\r
+                               memcpy(buf, outputString.c_str(), length);
                                        
                                MPI_File_write(outQuan, buf, length, MPI_CHAR, &status);
-                       
+                               delete buf;
+
                                MPI_File_close(&outQuan);
                        }
+
+                       delete FileName;
                #else
                        ofstream outQuan;
                        openOutputFile(file, outQuan);