1.9

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index b992750f1d4fafa1374c9a8a804758cd71ba9cfc..c94bf65f9e586eab7e99fc4bad2b0197cae54140 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -256,15 +256,18 @@ int FilterSeqsCommand::filterSequences() {
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
                                
-                               char outFilename[filteredFasta.length()];
-                               strcpy(outFilename, filteredFasta.c_str());
-                               
-                               char inFileName[fastafileNames[s].length()];
-                               strcpy(inFileName, fastafileNames[s].c_str());
+                               char* outFilename = new char[filteredFasta.length()];\r
+                               memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
+
+                               char* inFileName = new char[fastafileNames[s].length()];\r
+                               memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
                                
                                MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                                MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
                                
+                               delete inFileName;
+                               delete outFilename;
+
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 
                                if (pid == 0) { //you are the root process 
@@ -380,12 +383,13 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                
                        //read next sequence
                        int length = MPIPos[start+i+1] - MPIPos[start+i];
-                       char buf4[length];
+                       char* buf4 = new char[length];
                        MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
                        
                        string tempBuf = buf4;
                        if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
                        istringstream iss (tempBuf,istringstream::in);
+                       delete buf4;
        
                        Sequence seq(iss);  gobble(iss);
                        
@@ -405,11 +409,12 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                                if(count % 10 == 0){ //output to file 
                                        //send results to parent
                                        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_shared(outMPI, buf, length, MPI_CHAR, &status);
                                        outputString = "";
+                                       delete buf;
                                }
 
                        }
@@ -420,11 +425,12 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                if(outputString != ""){ //output to file 
                        //send results to parent
                        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_shared(outMPI, buf, length, MPI_CHAR, &status);
                        outputString = "";
+                       delete buf;
                }
                
                if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
@@ -692,11 +698,12 @@ string FilterSeqsCommand::createFilter() {
                MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD); 
        }else{
                //recieve filterString
-               char tempBuf[alignmentLength];
+               char* tempBuf = new char[alignmentLength];
                MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
                
                filterString = tempBuf;
                if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
+               delete tempBuf; 
        }
        
        MPI_Barrier(MPI_COMM_WORLD);
@@ -764,13 +771,14 @@ int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File&
                        //read next sequence
                        int length = MPIPos[start+i+1] - MPIPos[start+i];
        
-                       char buf4[length];
+                       char* buf4 = new char[length];
                        MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
                        
                        string tempBuf = buf4;
                        if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
                        istringstream iss (tempBuf,istringstream::in);
-       
+                       delete buf4;
+
                        Sequence seq(iss);  
 
                        if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }