X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=beea1bf915fccffa6b1f92e212e8125db6010af9;hb=ae57e166b2ed7b475ec3f466106bd76fabadd063;hp=34206a9460bf21eac543ee3d91031f8fe4af96ad;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 34206a9..beea1bf 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -8,11 +8,6 @@
  */
 
 #include "distancecommand.h"
-#include "ignoregaps.h"
-#include "eachgapdist.h"
-#include "eachgapignore.h"
-#include "onegapdist.h"
-#include "onegapignore.h"
 
 //**********************************************************************************************************************
 vector<string> DistanceCommand::setParameters(){	
@@ -152,6 +147,7 @@ DistanceCommand::DistanceCommand(string option) {
 				m->openInputFile(fastafile, inFASTA);
 				alignDB = SequenceDB(inFASTA); 
 				inFASTA.close();
+				m->setFastaFile(fastafile);
 			}
 			
 			oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
@@ -161,6 +157,7 @@ DistanceCommand::DistanceCommand(string option) {
 			column = validParameter.validFile(parameters, "column", true);
 			if (column == "not found") { column = ""; }
 			else if (column == "not open") { abort = true; }	
+			else { m->setColumnFile(column); }
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -198,26 +195,6 @@ DistanceCommand::DistanceCommand(string option) {
 			if ((column != "") && (oldfastafile != "") && (output != "column")) { m->mothurOut("You have provided column and oldfasta, indicating you want to append distances to your column file. Your output must be in column format to do so."); m->mothurOutEndLine(); abort=true; }
 			
 			if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
-			
-			ValidCalculators validCalculator;
-			
-			if (m->isTrue(countends) == true) {
-				for (int i=0; i<Estimators.size(); i++) {
-					if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
-						if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
-						else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
-						else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
-					}
-				}
-			}else {
-				for (int i=0; i<Estimators.size(); i++) {
-					if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
-						if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
-						else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
-						else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
-					}
-				}
-			}
 
 		}
 				
@@ -247,11 +224,13 @@ int DistanceCommand::execute(){
 		int numSeqs = alignDB.getNumSeqs();
 		cutoff += 0.005;
 		
+		if (!alignDB.sameLength()) {  m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
+		
 		string outputFile;
 				
 		if (output == "lt") { //does the user want lower triangle phylip formatted file 
 			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
-			remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
+			m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
 			
 			//output numSeqs to phylip formatted dist file
 		}else if (output == "column") { //user wants column format
@@ -264,10 +243,10 @@ int DistanceCommand::execute(){
 				rename(column.c_str(), tempcolumn.c_str());
 			}
 			
-			remove(outputFile.c_str());
+			m->mothurRemove(outputFile);
 		}else { //assume square
 			outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
-			remove(outputFile.c_str());
+			m->mothurRemove(outputFile);
 			outputTypes["phylip"].push_back(outputFile);
 		}
 		
@@ -338,7 +317,7 @@ int DistanceCommand::execute(){
 			
 				//do your part
 				string outputMyPart;
-				unsigned long int mySize;
+				unsigned long long mySize;
 				
 				if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
 				else { driverMPI(start, end, outputFile, mySize, output); }
@@ -360,7 +339,7 @@ int DistanceCommand::execute(){
 
 				//wait on chidren
 				for(int b = 1; b < processors; b++) { 
-					unsigned long int fileSize;
+					unsigned long long fileSize;
 					
 					if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
 					
@@ -388,7 +367,7 @@ int DistanceCommand::execute(){
 				MPI_File_close(&outMPI);
 			}else { //you are a child process
 				//do your part
-				unsigned long int size;
+				unsigned long long size;
 				if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
 				else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
 				
@@ -401,14 +380,14 @@ int DistanceCommand::execute(){
 		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else		
 				
-	#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+	//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		//if you don't need to fork anything
 		if(processors == 1){
 			if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
 			else { driver(0, numSeqs, outputFile, "square");  }
 		}else{ //you have multiple processors
 			
-			unsigned long int numDists = 0;
+			unsigned long long numDists = 0;
 			
 			if (output == "square") {
 				 numDists = numSeqs * numSeqs;
@@ -438,14 +417,14 @@ int DistanceCommand::execute(){
 			
 			createProcesses(outputFile); 
 		}
-	#else
+	//#else
 		//ifstream inFASTA;
-		if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
-		else { driver(0, numSeqs, outputFile, "square");  }
-	#endif
+		//if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
+		//else { driver(0, numSeqs, outputFile, "square");  }
+	//#endif
 	
 #endif
-		if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 		
 		#ifdef USE_MPI
 			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
@@ -468,17 +447,17 @@ int DistanceCommand::execute(){
 			if (outputFile == column) { 
 				string tempcolumn = column + ".old";
 				m->appendFiles(tempcolumn, outputFile);
-				remove(tempcolumn.c_str());
+				m->mothurRemove(tempcolumn);
 			}else{
 				m->appendFiles(outputFile, column);
-				remove(outputFile.c_str());
+				m->mothurRemove(outputFile);
 				outputFile = column;
 			}
 			
 			if (outputDir != "") { 
 				string newOutputName = outputDir + m->getSimpleName(outputFile);
 				rename(outputFile.c_str(), newOutputName.c_str());
-				remove(outputFile.c_str());
+				m->mothurRemove(outputFile);
 				outputFile = newOutputName;
 			}
 		}
@@ -488,9 +467,7 @@ int DistanceCommand::execute(){
 			}
 		#endif
 		
-		if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
-		
-		delete distCalculator;
+		if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFile); return 0; }
 		
 		//set phylip file as new current phylipfile
 		string current = "";
@@ -563,25 +540,80 @@ void DistanceCommand::createProcesses(string filename) {
 			int temp = processIDS[i];
 			wait(&temp);
 		}
+#else
+		//////////////////////////////////////////////////////////////////////////////////////////////////////
+		//Windows version shared memory, so be careful when passing variables through the distanceData struct. 
+		//Above fork() will clone, so memory is separate, but that's not the case with windows, 
+		//that's why the distance calculator was moved inside of the driver to make separate copies.
+		//////////////////////////////////////////////////////////////////////////////////////////////////////
+		
+		vector<distanceData*> pDataArray; //[processors-1];
+		DWORD   dwThreadIdArray[processors-1];
+		HANDLE  hThreadArray[processors-1]; 
+		
+		//Create processor-1 worker threads.
+		for( int i=0; i<processors-1; i++ ){
+			
+			// Allocate memory for thread data.
+			distanceData* tempDist = new distanceData(lines[i+1].start, lines[i+1].end, (filename + toString(i) + ".temp"), cutoff, alignDB, Estimators, m, output, numNewFasta, countends);
+			pDataArray.push_back(tempDist);
+			processIDS.push_back(i);
+			
+			//MyDistThreadFunction is in header. It must be global or static to work with the threads.
+			//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+			hThreadArray[i] = CreateThread(NULL, 0, MyDistThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
+		}
+		
+		//do your part
+		if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
+		else { driver(lines[0].start, lines[0].end, filename, "square"); }
+		
+		//Wait until all threads have terminated.
+		WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+		
+		//Close all thread handles and free memory allocations.
+		for(int i=0; i < pDataArray.size(); i++){
+			CloseHandle(hThreadArray[i]);
+			delete pDataArray[i];
+		}
+#endif
 		
 		//append and remove temp files
 		for (int i=0;i<processIDS.size();i++) { 
 			m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
-			remove((filename + toString(processIDS[i]) + ".temp").c_str());
+			m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 		}
-#endif
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "DistanceCommand", "createProcesses");
 		exit(1);
 	}
 }
-
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
 int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
 	try {
-
+		ValidCalculators validCalculator;
+		Dist* distCalculator;
+		if (m->isTrue(countends) == true) {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+					else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
+					else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
+				}
+			}
+		}else {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+					else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+					else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+				}
+			}
+		}
+		
 		int startTime = time(NULL);
 		
 		//column file
@@ -601,7 +633,7 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, float
 			}
 			for(int j=0;j<i;j++){
 				
-				if (m->control_pressed) { outFile.close(); return 0;  }
+				if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 				
 				//if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
 				//the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
@@ -626,6 +658,7 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, float
 		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 		
 		outFile.close();
+		delete distCalculator;
 		
 		return 1;
 	}
@@ -638,7 +671,26 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, float
 /////// need to fix to work with calcs and sequencedb
 int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
 	try {
-
+		ValidCalculators validCalculator;
+		Dist* distCalculator;
+		if (m->isTrue(countends) == true) {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+					else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
+					else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
+				}
+			}
+		}else {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+					else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+					else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+				}
+			}
+		}
+		
 		int startTime = time(NULL);
 		
 		//column file
@@ -658,7 +710,7 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, string
 			
 			for(int j=0;j<alignDB.getNumSeqs();j++){
 				
-				if (m->control_pressed) { outFile.close(); return 0;  }
+				if (m->control_pressed) { delete distCalculator; outFile.close(); return 0;  }
 				
 				distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 				double dist = distCalculator->getDist();
@@ -676,6 +728,7 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, string
 		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 		
 		outFile.close();
+		delete distCalculator;
 		
 		return 1;
 	}
@@ -689,6 +742,28 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, string
 /////// need to fix to work with calcs and sequencedb
 int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
 	try {
+		
+		ValidCalculators validCalculator;
+		Dist* distCalculator;
+		if (m->isTrue(countends) == true) {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+					else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
+					else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
+				}
+			}
+		}else {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+					else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+					else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+				}
+			}
+		}
+		
+		
 		MPI_Status status;
 		int startTime = time(NULL);
 		
@@ -698,7 +773,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
 	
 			for(int j=0;j<i;j++){
 				
-				if (m->control_pressed) {  return 0;  }
+				if (m->control_pressed) {  delete distCalculator; return 0;  }
 				
 				//if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
 				//the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
@@ -731,7 +806,8 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
 		}
 		
 		//m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-		cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;		
+		cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;	
+		delete distCalculator;
 		return 1;
 	}
 	catch(exception& e) {
@@ -741,8 +817,29 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
 	try {
+		ValidCalculators validCalculator;
+		Dist* distCalculator;
+		if (m->isTrue(countends) == true) {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+					else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
+					else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
+				}
+			}
+		}else {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+					else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+					else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+				}
+			}
+		}
+		
+		
 		MPI_Status status;
 		
 		MPI_File outMPI;
@@ -774,7 +871,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 			
 			for(int j=0;j<i;j++){
 				
-				if (m->control_pressed) {  return 0;  }
+				if (m->control_pressed) { delete distCalculator; return 0;  }
 				
 				distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 				double dist = distCalculator->getDist();
@@ -805,6 +902,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 		//m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 		cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 		MPI_File_close(&outMPI);
+		delete distCalculator;
 		
 		return 1;
 	}
@@ -815,8 +913,28 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
 	try {
+		ValidCalculators validCalculator;
+		Dist* distCalculator;
+		if (m->isTrue(countends) == true) {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+					else if (Estimators[i] == "eachgap")	{	distCalculator = new eachGapDist();	}
+					else if (Estimators[i] == "onegap")		{	distCalculator = new oneGapDist();	}
+				}
+			}
+		}else {
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) { 
+					if (Estimators[i] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+					else if (Estimators[i] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+					else if (Estimators[i] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+				}
+			}
+		}
+		
 		MPI_Status status;
 		
 		MPI_File outMPI;
@@ -848,7 +966,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 			
 			for(int j=0;j<alignDB.getNumSeqs();j++){
 				
-				if (m->control_pressed) {  return 0;  }
+				if (m->control_pressed) { delete distCalculator; return 0;  }
 				
 				distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
 				double dist = distCalculator->getDist();
@@ -879,7 +997,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 		//m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
 		cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
 		MPI_File_close(&outMPI);
-		
+		delete distCalculator;
 		return 1;
 	}
 	catch(exception& e) {
@@ -931,7 +1049,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
 		//m->openInputFile(outfile, in);
 		
 		while(!in.eof()) {
-			if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+			if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
 			
 			in >> first >> second >> dist; m->gobble(in);
 				
@@ -966,7 +1084,7 @@ int DistanceCommand::convertMatrix(string outputFile) {
 		in.close();
 		out.close();
 		
-		remove(outfile.c_str());
+		m->mothurRemove(outfile);
 		
 		return 1;
 		
@@ -1021,7 +1139,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
 		//m->openInputFile(outfile, in);
 		
 		while(!in.eof()) {
-			if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+			if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
 			
 			in >> first >> second >> dist; m->gobble(in);
 				
@@ -1060,7 +1178,7 @@ int DistanceCommand::convertToLowerTriangle(string outputFile) {
 		in.close();
 		out.close();
 		
-		remove(outfile.c_str());
+		m->mothurRemove(outfile);
 		
 		return 1;
 		
@@ -1131,7 +1249,7 @@ bool DistanceCommand::sanityCheck() {
 		string name1, name2;
 		float dist;
 		while (!inDist.eof()) {
-			if (m->control_pressed) {  inDist.close(); outDist.close(); remove(outputFile.c_str()); return good;  }
+			if (m->control_pressed) {  inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good;  }
 		
 			inDist >> name1 >> name2 >> dist; m->gobble(inDist);
 			
@@ -1148,10 +1266,10 @@ bool DistanceCommand::sanityCheck() {
 		outDist.close();
 		
 		if (good) {
-			remove(column.c_str());
+			m->mothurRemove(column);
 			rename(outputFile.c_str(), column.c_str());
 		}else{
-			remove(outputFile.c_str()); //temp file is bad because file mismatch above
+			m->mothurRemove(outputFile); //temp file is bad because file mismatch above
 		}
 		
 		return good;