X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pintail.cpp;h=b9f2434d19d4cc842bfac1dce4f6de5a0d1b742d;hp=c0ea90436628e8a86dbce69f894d8f3a353b7a27;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=1d7a10dc3dafd1606d6255bdb54e02429cbee47c

diff --git a/pintail.cpp b/pintail.cpp
index c0ea904..b9f2434 100644
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -74,7 +74,7 @@ int Pintail::doPrep() {
 	#ifdef USE_MPI
 		//do nothing
 	#else
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			//find breakup of templatefile for quantiles
 			if (processors == 1) {   templateLines.push_back(new linePair(0, templateSeqs.size()));  }
 			else { 
@@ -170,13 +170,13 @@ int Pintail::doPrep() {
 			string noOutliers, outliers;
 			
 			if ((!filter) && (seqMask == "")) {
-				noOutliers = templateFileName + "pintail.quan";
+				noOutliers = m->getRootName(m->getSimpleName(templateFileName)) + "pintail.quan";
 			}else if ((!filter) && (seqMask != "")) { 
-				noOutliers =templateFileName + "pintail.masked.quan";
+				noOutliers =m->getRootName(m->getSimpleName(templateFileName)) + "pintail.masked.quan";
 			}else if ((filter) && (seqMask != "")) { 
-				noOutliers = templateFileName + "pintail.filtered." + m->getSimpleName(m->getRootName(fastafile)) + "masked.quan";
+				noOutliers = m->getRootName(m->getSimpleName(templateFileName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastafile)) + "masked.quan";
 			}else if ((filter) && (seqMask == "")) { 
-				noOutliers = templateFileName + "pintail.filtered." + m->getSimpleName(m->getRootName(fastafile)) + "quan";
+				noOutliers = m->getRootName(m->getSimpleName(templateFileName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastafile)) + "quan";
 			}
 
 			decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
@@ -249,8 +249,9 @@ int Pintail::doPrep() {
 	}
 }
 //***************************************************************************************************************
-int Pintail::print(ostream& out, ostream& outAcc) {
+Sequence Pintail::print(ostream& out, ostream& outAcc) {
 	try {
+		
 		int index = ceil(deviation);
 		
 		//is your DE value higher than the 95%
@@ -279,7 +280,7 @@ int Pintail::print(ostream& out, ostream& outAcc) {
 		for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
 		out << endl;
 		
-		return 0;
+		return *querySeq;
 		
 	}
 	catch(exception& e) {
@@ -289,9 +290,9 @@ int Pintail::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int Pintail::print(MPI_File& out, MPI_File& outAcc) {
+Sequence Pintail::print(MPI_File& out, MPI_File& outAcc) {
 	try {
-		bool results = false;
+		
 		string outputString = "";
 		int index = ceil(deviation);
 		
@@ -319,7 +320,7 @@ int Pintail::print(MPI_File& out, MPI_File& outAcc) {
 			MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 			delete buf;
 
-			results = true;
+			return *querySeq;
 		}
 		outputString += "Observed\t";
 		
@@ -339,7 +340,7 @@ int Pintail::print(MPI_File& out, MPI_File& outAcc) {
 		MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 		delete buf2;
 		
-		return results;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Pintail", "print");
@@ -528,7 +529,7 @@ Sequence* Pintail::findPairs(Sequence* q) {
 //**************************************************************************************************
 void Pintail::createProcessesQuan() {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 1;
 		vector<int> processIDS;
 				
@@ -560,7 +561,11 @@ void Pintail::createProcessesQuan() {
 				out.close();
 				
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0);
+			}
 		}
 		
 		//parent does its part
@@ -607,7 +612,7 @@ void Pintail::createProcessesQuan() {
 			}
 					
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 
 #else