X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pintail.cpp;h=b9f2434d19d4cc842bfac1dce4f6de5a0d1b742d;hp=b04efea9ba2c59b06dff4bf599d492dc2f9cd0e2;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=4b6e3f7b5543822a2cca4fb076ab6af2ce8ca62d

diff --git a/pintail.cpp b/pintail.cpp
index b04efea..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());
@@ -249,7 +249,7 @@ int Pintail::doPrep() {
 	}
 }
 //***************************************************************************************************************
-Sequence* Pintail::print(ostream& out, ostream& outAcc) {
+Sequence Pintail::print(ostream& out, ostream& outAcc) {
 	try {
 		
 		int index = ceil(deviation);
@@ -280,7 +280,7 @@ Sequence* Pintail::print(ostream& out, ostream& outAcc) {
 		for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
 		out << endl;
 		
-		return NULL;
+		return *querySeq;
 		
 	}
 	catch(exception& e) {
@@ -290,7 +290,7 @@ Sequence* Pintail::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-Sequence* Pintail::print(MPI_File& out, MPI_File& outAcc) {
+Sequence Pintail::print(MPI_File& out, MPI_File& outAcc) {
 	try {
 		
 		string outputString = "";
@@ -320,7 +320,7 @@ Sequence* Pintail::print(MPI_File& out, MPI_File& outAcc) {
 			MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 			delete buf;
 
-			return NULL;
+			return *querySeq;
 		}
 		outputString += "Observed\t";
 		
@@ -340,7 +340,7 @@ Sequence* Pintail::print(MPI_File& out, MPI_File& outAcc) {
 		MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 		delete buf2;
 		
-		return NULL;
+		return *querySeq;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Pintail", "print");
@@ -529,7 +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;
 				
@@ -612,7 +612,7 @@ void Pintail::createProcessesQuan() {
 			}
 					
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
 
 #else