working on testing

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 4ad60c50742e36c630fbbc81a7f1f73ad527ec42..2362eb5ac80416f6aa86d8b7d011e275d7d3a88d 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -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 = templateFileName + "pintail.quan";
                        }else if ((!filter) && (seqMask != "")) { 
-                               noOutliers = outputDir + m->getRootName(m->getSimpleName(templateFileName)) + "pintail.masked.quan";
+                               noOutliers =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 = 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 = templateFileName + "pintail.filtered." + m->getSimpleName(m->getRootName(fastafile)) + "quan";
                        }
 
                        decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());