Thallinger changes to cluster command.

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index b7e5b5fb137fa45b977766c713efafb9bee03cef..bca7df96deabdd28a8f9e83423b6c1608073215e 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -34,6 +34,11 @@ void Pintail::print(ostream& out) {
                for (int i = 0; i < querySeqs.size(); i++) {
                        
                        int index = ceil(deviation[i]);
+float quan = 2.64 * log10(deviation[i]) + 1.46;
+cout << "dist = " << index << endl;
+cout << "de = "  << DE[i] << endl;
+cout << "mallard quantile = " << quan << endl;
+cout << "my quantile = " << quantiles[index][4] << endl;
                        
                        //is your DE value higher than the 95%
                        string chimera;
@@ -158,7 +163,7 @@ void Pintail::getChimeras() {
                }else                           {   probabilityProfile = readFreq();                      }
 
                //make P into Q
-               for (int i = 0; i < probabilityProfile.size(); i++)  {  probabilityProfile[i] = 1 - probabilityProfile[i];       cout << i << '\t' << probabilityProfile[i] << endl;  }
+               for (int i = 0; i < probabilityProfile.size(); i++)  {  probabilityProfile[i] = 1 - probabilityProfile[i];   }  //cout << i << '\t' << probabilityProfile[i] << endl;
                mothurOut("Done."); mothurOutEndLine();
                
                //mask querys
@@ -270,6 +275,9 @@ cout << querySeqs[i]->getName() << '\t' << "dist value = " << dist << endl;
                                quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
                        }else {         createProcessesQuan();          }
                        
+                       
+                       decalc->removeObviousOutliers(quantiles);
+                       
                        ofstream out4;
                        string o = getRootName(templateFile) + "quan";
                        
@@ -344,7 +352,7 @@ vector<float> Pintail::readFreq() {
                        
                        in >> pos >> num;
                        
-                       if (h.count(pos-1) > 0) {
+                       if (h.count(pos) > 0) {
                                float Pi;
                                Pi =  (num - 0.25) / 0.75;