added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 2698fe48b278fff835ec9c1a5c40dfe8dc76a9f3..6adfdf91ebeaf30847bee05d90f2c9b22d3c5946 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -18,7 +18,7 @@ inline bool compareQuanMembers(quanMember left, quanMember right){
 } 
 //***************************************************************************************************************
 
-Pintail::Pintail(string filename, string temp) {  fastafile = filename;  templateFile = temp;  }
+Pintail::Pintail(string filename, string temp, string o) {  fastafile = filename;  templateFile = temp; outputDir = o; }
 //***************************************************************************************************************
 
 Pintail::~Pintail() {
@@ -161,7 +161,7 @@ int Pintail::getChimeras() {
                mothurOut("Getting conservation... "); cout.flush();
                if (consfile == "") { 
                        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, templateFile); 
+                       probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFile)); 
                        mothurOut("Done."); mothurOutEndLine();
                }else                           {   probabilityProfile = readFreq();                      }
 
@@ -281,13 +281,13 @@ int Pintail::getChimeras() {
                        string noOutliers, outliers;
                        
                        if ((!filter) && (seqMask == "")) {
-                               noOutliers = getRootName(templateFile) + "pintail.quan";
+                               noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.quan";
                        }else if ((filter) && (seqMask == "")) { 
-                               noOutliers = getRootName(templateFile) + "pintail.filtered.quan";
+                               noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.quan";
                        }else if ((!filter) && (seqMask != "")) { 
-                               noOutliers = getRootName(templateFile) + "pintail.masked.quan";
+                               noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.masked.quan";
                        }else if ((filter) && (seqMask != "")) { 
-                               noOutliers = getRootName(templateFile) + "pintail.filtered.masked.quan";
+                               noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.masked.quan";
                        }
 
                        //outliers = getRootName(templateFile) + "pintail.quanYESOUTLIERS";