1.9

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 1a5ae09df87ee9e37abbf81621b0da532a4549dd..777584bf0c75cdc8f26d5125defa5e20f296ce6e 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -8,10 +8,6 @@
  */
 
 #include "chimeraslayercommand.h"
-#include "bellerophon.h"
-#include "pintail.h"
-#include "ccode.h"
-#include "chimeracheckrdp.h"
 #include "chimeraslayer.h"
 
 
@@ -220,20 +216,24 @@ int ChimeraSlayerCommand::execute(){
                        
                        int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                        int inMode=MPI_MODE_RDONLY; 
-                                                       
-                       char outFilename[outputFileName.length()];
-                       strcpy(outFilename, outputFileName.c_str());
                        
-                       char outAccnosFilename[accnosFileName.length()];
-                       strcpy(outAccnosFilename, accnosFileName.c_str());
+                       char* outFilename = new char[outputFileName.length()];\r
+                       memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
                        
-                       char inFileName[fastafile.length()];
-                       strcpy(inFileName, fastafile.c_str());
+                       char* outAccnosFilename = new char[accnosFileName.length()];\r
+                       memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+
+                       char* inFileName = new char[fastafile.length()];\r
+                       memcpy(inFileName, fastafile.c_str(), fastafile.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);
                        MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
                        
+                       delete inFileName;
+                       delete outFilename;
+                       delete outAccnosFilename;
+
                        if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 
                
@@ -246,10 +246,12 @@ int ChimeraSlayerCommand::execute(){
                                
                                //print header
                                int length = outTemp.length();
-                               char buf2[length];
-                               strcpy(buf2, outTemp.c_str()); 
+                               char* buf2 = new char[length];\r
+                               memcpy(buf2, outTemp.c_str(), length);
+
                                MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
-                               
+                               delete buf2;
+
                                MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
                                
                                //send file positions to all processes
@@ -521,12 +523,13 @@ int ChimeraSlayerCommand::driverMPI(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* candidateSeq = new Sequence(iss);  gobble(iss);