X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefact.cpp;h=83a6306db7568ac228fb110f1ad1c405cec9c7ec;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=d8a6b5cc2be05f8022da2c9234a358bb6fa98e8c;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/rarefact.cpp b/rarefact.cpp
index d8a6b5c..83a6306 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -24,7 +24,7 @@ int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
 		if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
 		else { increment = percentFreq;  }	
 		
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				if(processors == 1){
 					driver(rcd, increment, nIters);	
 				}else{
@@ -86,12 +86,12 @@ int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000
 				lookup->set(binNumber, abundance);
 				rank->set(abundance, rank->get(abundance)+1);
 
-				if((i == 0) || (i+1) % increment == 0){
+				if((i == 0) || ((i+1) % increment == 0) || (ends.count(i+1) != 0)){
 					rcd->updateRankData(rank);
 				}
 			}
 	
-			if(numSeqs % increment != 0){
+			if((numSeqs % increment != 0) || (ends.count(numSeqs) != 0)){
 				rcd->updateRankData(rank);
 			}
 
@@ -114,7 +114,7 @@ int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000
 
 int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		
 		vector<int> processIDS;
@@ -123,7 +123,7 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
-			int pid = fork();
+			pid_t pid = fork();
 			
 			if (pid > 0) {
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
@@ -133,7 +133,7 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
 			
 				//pass numSeqs to parent
 				for(int i=0;i<displays.size();i++){
-					string tempFile = toString(getpid()) + toString(i) + ".rarefact.temp";
+					string tempFile = m->mothurGetpid(process) + toString(i) + ".rarefact.temp";
 					displays[i]->outputTempFiles(tempFile);
 				}
 				exit(0);
@@ -157,7 +157,7 @@ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd,
 			for(int j=0;j<displays.size();j++){
 				string s = toString(processIDS[i]) + toString(j) + ".rarefact.temp";
 				displays[j]->inputTempFiles(s);
-				remove(s.c_str());
+				m->mothurRemove(s);
 			}
 		}