X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=0b96f2172359efc9b7ed5ab5c9dcc15e7223dbbc;hb=a61980e36d61937acccadc41be260165a1e389f4;hp=6958c00187ba5a41bec3db7ceb9b3fe25deb5005;hpb=813f0516e9c7533859f57ebe6d7b8854896bf009;p=mothur.git

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 6958c00..0b96f21 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -191,22 +191,31 @@ int ChimeraCcodeCommand::execute(){
 			int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
 			int inMode=MPI_MODE_RDONLY; 
 
-			char* outFilename = new char[outputFileName.length()];
-			memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+			//char* outFilename = new char[outputFileName.length()];
+			//memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
 			
-			char* outAccnosFilename = new char[accnosFileName.length()];
-			memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+			char outFilename[1024];
+			strcpy(outFilename, outputFileName.c_str());
+			
+			//char* outAccnosFilename = new char[accnosFileName.length()];
+			//memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+			
+			char outAccnosFilename[1024];
+			strcpy(outAccnosFilename, accnosFileName.c_str());
 
-			char* inFileName = new char[fastafile.length()];
-			memcpy(inFileName, fastafile.c_str(), fastafile.length());
+			//char* inFileName = new char[fastafile.length()];
+			//memcpy(inFileName, fastafile.c_str(), fastafile.length());
+			
+			char inFileName[1024];
+			strcpy(inFileName, fastafile.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);
 			MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 			
-			delete inFileName;
-			delete outFilename;
-			delete outAccnosFilename;
+			//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;  }
 		
@@ -215,7 +224,7 @@ int ChimeraCcodeCommand::execute(){
 				
 				//print header
 				int length = outTemp.length();
-				char* buf2 = new char[length];
+				char* buf2 = new char[length];
 				memcpy(buf2, outTemp.c_str(), length);
 
 				MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
@@ -499,7 +508,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 			//read next sequence
 			int length = MPIPos[start+i+1] - MPIPos[start+i];
 	
-			char* buf4 = new char[length];
+			char* buf4 = new char[length];
 				
 			MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);