a few modifications for 1.9

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index c94bf65f9e586eab7e99fc4bad2b0197cae54140..b64e2f530ff91af78cc69dea71b9d2f53f3f981b 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -256,17 +256,23 @@ int FilterSeqsCommand::filterSequences() {
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
                                
-                               char* outFilename = new char[filteredFasta.length()];\r
-                               memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
+                               //char* outFilename = new char[filteredFasta.length()];
+                               //memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
+                               
+                               char outFilename[1024];
+                               strcpy(outFilename, filteredFasta.c_str());
 
-                               char* inFileName = new char[fastafileNames[s].length()];\r
-                               memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
+                               //char* inFileName = new char[fastafileNames[s].length()];
+                               //memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
+                               
+                               char inFileName[1024];
+                               strcpy(inFileName, fastafileNames[s].c_str());
                                
                                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;
+                               //delete inFileName;
+                               //delete outFilename;
 
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 
@@ -409,7 +415,7 @@ 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 = new char[length];\r
+                                       char* buf = new char[length];
                                        memcpy(buf, outputString.c_str(), length);
                                
                                        MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
@@ -425,7 +431,7 @@ 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 = new char[length];\r
+                       char* buf = new char[length];
                        memcpy(buf, outputString.c_str(), length);
                        
                        MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
@@ -554,8 +560,11 @@ string FilterSeqsCommand::createFilter() {
                                MPI_Comm_size(MPI_COMM_WORLD, &processors);
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
                                                        
-                               char* tempFileName = new char(fastafileNames[s].length());
-                               tempFileName = &(fastafileNames[s][0]);
+                               //char* tempFileName = new char(fastafileNames[s].length());
+                               //tempFileName = &(fastafileNames[s][0]);
+                               
+                               char tempFileName[1024];
+                               strcpy(tempFileName, fastafileNames[s].c_str());
                
                                MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer