1.9

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index 692a4fee837376232981cfaf91934b96b5efa75d..32351f942eaea499f321720bb36caf335f68d306 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -108,12 +108,13 @@ vector<Sequence*> Chimera::readSeqs(string file) {
                        MPI_Status status; 
                        MPI_File inMPI;
                        MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-       
-                       char inFileName[file.length()];
-                       strcpy(inFileName, file.c_str());
+
+                       char* inFileName = new char[file.length()];\r
+                       memcpy(inFileName, file.c_str(), file.length());
        
                        MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
-       
+                       delete inFileName;
+
                        if (pid == 0) {
                                positions = setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
 
@@ -133,12 +134,14 @@ vector<Sequence*> Chimera::readSeqs(string file) {
        
                                //read next sequence
                                int seqlength = positions[i+1] - positions[i];
-                               char buf4[seqlength];
+                               char* buf4 = new char[seqlength];
+
                                MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
                                
                                string tempBuf = buf4;
                                if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
-                               
+                               delete buf4;
+
                                istringstream iss (tempBuf,istringstream::in);
                
                                Sequence* current = new Sequence(iss);   
@@ -196,18 +199,22 @@ void Chimera::setMask(string filename) {
                        MPI_Offset size;
                        MPI_Status status;
                        
-                       char inFileName[filename.length()];
-                       strcpy(inFileName, filename.c_str());
+                       char* inFileName = new char[filename.length()];\r
+                       memcpy(inFileName, filename.c_str(), filename.length());
        
                        MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                        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;
                        
                        if (!iss.eof()) {
                                Sequence temp(iss);