X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;fp=chimeracheckcommand.cpp;h=2b88eb5736bfd37364461facb043b0db76aa3cfc;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=584e9874fd4cea4136d45c184a4c0662973c3b25;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 584e987..2b88eb5 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -370,7 +370,7 @@ int ChimeraCheckCommand::execute(){
 				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);
 				
-				if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} outputTypes.clear(); delete chimera; return 0;  }
+				if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear(); delete chimera; return 0;  }
 				
 				if (pid == 0) { //you are the root process 
 					MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
@@ -390,7 +390,7 @@ int ChimeraCheckCommand::execute(){
 					//align your part
 					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 					
-					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}   outputTypes.clear(); delete chimera; return 0;  }
+					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}   outputTypes.clear(); delete chimera; return 0;  }
 					
 					//wait on chidren
 					for(int j = 1; j < processors; j++) { 
@@ -410,7 +410,7 @@ int ChimeraCheckCommand::execute(){
 					//align your part
 					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 					
-					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}  outputTypes.clear(); delete chimera; return 0;  }
+					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  outputTypes.clear(); delete chimera; return 0;  }
 					
 					//tell parent you are done.
 					char buf[5];
@@ -435,7 +435,7 @@ int ChimeraCheckCommand::execute(){
 				if(processors == 1){
 					numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 					
-					if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} for (int j = 0; j < lines.size(); j++) {  delete lines[j];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
+					if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} for (int j = 0; j < lines.size(); j++) {  delete lines[j];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
 									
 				}else{
 					processIDS.resize(0);
@@ -447,11 +447,11 @@ int ChimeraCheckCommand::execute(){
 					//append output files
 					for(int j=1;j<processors;j++){
 						m->appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
-						remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
+						m->mothurRemove((outputFileName + toString(processIDS[j]) + ".temp"));
 					}
 					
 					if (m->control_pressed) { 
-						for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} outputTypes.clear();
+						for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear();
 						for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 						delete chimera;
 						return 0;
@@ -461,7 +461,7 @@ int ChimeraCheckCommand::execute(){
 			#else
 				numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 				
-				if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} outputTypes.clear(); delete chimera; return 0; }
+				if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear(); delete chimera; return 0; }
 			#endif
 		#endif		
 			delete chimera;
@@ -636,7 +636,7 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename)
 			string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 			m->openInputFile(tempFile, in);
 			if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
-			in.close(); remove(tempFile.c_str());
+			in.close(); m->mothurRemove(tempFile);
 		}
 		
 		return num;