X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bellerophon.cpp;h=833cfb907d6d4bd2aed8acb3d8522932ac3b2e7d;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=f4d04ea074b1d2d95cb9bcff4fcc3084e7f234c6;hpb=4b6e3f7b5543822a2cca4fb076ab6af2ce8ca62d;p=mothur.git

diff --git a/bellerophon.cpp b/bellerophon.cpp
index f4d04ea..833cfb9 100644
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -246,7 +246,7 @@ int Bellerophon::getChimeras() {
 		numSeqsPerProcessor = iters / processors;
 		
 		//each process hits this only once
-		unsigned long int startPos = pid * numSeqsPerProcessor;
+		unsigned long long startPos = pid * numSeqsPerProcessor;
 		if(pid == processors - 1){
 				numSeqsPerProcessor = iters - pid * numSeqsPerProcessor;
 		}
@@ -274,7 +274,7 @@ int Bellerophon::getChimeras() {
 					MPI_Recv(&length, 1, MPI_INT, j, 2001, MPI_COMM_WORLD, &status);
 					
 					char* buf = new char[length];
-					MPI_Recv(&buf, length, MPI_CHAR, j, 2001, MPI_COMM_WORLD, &status);
+					MPI_Recv(&buf[0], length, MPI_CHAR, j, 2001, MPI_COMM_WORLD, &status);
 					
 					string temp = buf;
 					if (temp.length() > length) { temp = temp.substr(0, length); }
@@ -293,7 +293,7 @@ int Bellerophon::getChimeras() {
 			//played with this a bit, but it may be better to try user-defined datatypes with set string lengths??
 			vector<string> MPIBestSend = getBestWindow(lines[0]);
 			pref.clear();
-			
+				
 			//send your result to parent
 			for (int i = 0; i < numSeqs; i++) {
 				
@@ -314,7 +314,7 @@ int Bellerophon::getChimeras() {
 	#else
 	
 		//divide breakpoints between processors
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			if(processors == 1){ 
 				lines.push_back(linePair(0, iters));	
 				
@@ -326,7 +326,7 @@ int Bellerophon::getChimeras() {
 				int numSeqsPerProcessor = iters / processors;
 				
 				for (int i = 0; i < processors; i++) {
-					unsigned long int startPos = i * numSeqsPerProcessor;
+					unsigned long long startPos = i * numSeqsPerProcessor;
 					if(i == processors - 1){
 						numSeqsPerProcessor = iters - i * numSeqsPerProcessor;
 					}
@@ -356,7 +356,7 @@ int Bellerophon::getChimeras() {
 
 int Bellerophon::createProcesses(vector<int> mid) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 0;
 		int exitCommand = 1;
 		vector<int> processIDS;
@@ -677,7 +677,7 @@ int Bellerophon::writePrefs(string file, linePair tempLine) {
 			
 			for (int j = 0; j < numSeqs; j++) {
 				
-				if (m->control_pressed) { outTemp.close(); remove(file.c_str()); return 0; }
+				if (m->control_pressed) { outTemp.close(); m->mothurRemove(file); return 0; }
 				
 				outTemp << pref[i][j].name << '\t' << pref[i][j].leftParent << '\t' << pref[i][j].rightParent << '\t';
 				outTemp << pref[i][j].score << '\t' << pref[i][j].closestLeft << '\t' << pref[i][j].closestRight << '\t' << pref[i][j].midpoint <<  endl;
@@ -709,7 +709,7 @@ int Bellerophon::readPrefs(string file) {
 			
 			for (int j = 0; j < numSeqs; j++) {
 				
-				if (m->control_pressed) { inTemp.close(); remove(file.c_str()); return 0; }
+				if (m->control_pressed) { inTemp.close(); m->mothurRemove(file); return 0; }
 			
 				inTemp >> pref[i][j].name >> pref[i][j].leftParent >> pref[i][j].rightParent;
 				inTemp >> pref[i][j].score >> pref[i][j].closestLeft >> pref[i][j].closestRight >> pref[i][j].midpoint;
@@ -719,7 +719,7 @@ int Bellerophon::readPrefs(string file) {
 		
 		inTemp.close();
 		
-		remove(file.c_str());
+		m->mothurRemove(file);
 		
 		return 0;
 	}