added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 10f931f8230d035decdfcc282fe8de248aa0bdac..af64c25ce290a808a5edc8295645bc16bf277856 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -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());
@@ -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");
@@ -612,7 +612,7 @@ void Pintail::createProcessesQuan() {
                        }
                                        
                        in.close();
-                       remove(s.c_str());
+                       m->mothurRemove(s);
                }
 
 #else