X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pintail.cpp;h=b9f2434d19d4cc842bfac1dce4f6de5a0d1b742d;hp=4ad60c50742e36c630fbbc81a7f1f73ad527ec42;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6

diff --git a/pintail.cpp b/pintail.cpp
index 4ad60c5..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 { 
@@ -92,7 +92,7 @@ int Pintail::doPrep() {
 		m->mothurOut("Getting conservation... "); cout.flush();
 		if (consfile == "") { 
 			m->mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
-			probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + m->getSimpleName(templateFileName)); 
+			probabilityProfile = decalc->calcFreq(templateSeqs, templateFileName); 
 			if (m->control_pressed) {  return 0;  }
 			m->mothurOut("Done."); m->mothurOutEndLine();
 		}else				{   probabilityProfile = readFreq();	m->mothurOut("Done.");		  }
@@ -170,13 +170,13 @@ int Pintail::doPrep() {
 			string noOutliers, outliers;
 			
 			if ((!filter) && (seqMask == "")) {
-				noOutliers = outputDir + m->getRootName(m->getSimpleName(templateFileName)) + "pintail.quan";
+				noOutliers = m->getRootName(m->getSimpleName(templateFileName)) + "pintail.quan";
 			}else if ((!filter) && (seqMask != "")) { 
-				noOutliers = outputDir + m->getRootName(m->getSimpleName(templateFileName)) + "pintail.masked.quan";
+				noOutliers =m->getRootName(m->getSimpleName(templateFileName)) + "pintail.masked.quan";
 			}else if ((filter) && (seqMask != "")) { 
-				noOutliers = outputDir + m->getRootName(m->getSimpleName(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 = outputDir + m->getRootName(m->getSimpleName(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");
@@ -528,8 +529,8 @@ Sequence* Pintail::findPairs(Sequence* q) {
 //**************************************************************************************************
 void Pintail::createProcessesQuan() {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		int process = 0;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+		int process = 1;
 		vector<int> processIDS;
 				
 		//loop through and create all the processes you want
@@ -547,7 +548,6 @@ void Pintail::createProcessesQuan() {
 				ofstream out;
 				string s = toString(getpid()) + ".temp";
 				m->openOutputFile(s, out);
-				
 								
 				//output observed distances
 				for (int i = 0; i < quantilesMembers.size(); i++) {
@@ -561,17 +561,24 @@ 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
+		quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[0]->start, templateLines[0]->end);
+		
 		//force parent to wait until all the processes are done
-		for (int i=0;i<processors;i++) { 
+		for (int i=0;i<(processors-1);i++) { 
 			int temp = processIDS[i];
 			wait(&temp);
 		}
 
 		//get data created by processes
-		for (int i=0;i<processors;i++) { 
+		for (int i=0;i<(processors-1);i++) { 
 			ifstream in;
 			string s = toString(processIDS[i]) + ".temp";
 			m->openInputFile(s, in);
@@ -605,9 +612,9 @@ void Pintail::createProcessesQuan() {
 			}
 					
 			in.close();
-			remove(s.c_str());
+			m->mothurRemove(s);
 		}
-		
+
 #else
 		quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 #endif