sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index cf70010e76a6b9cba77b8ade2fcd7d18713391d3..6eaab6f2f974f8e1036561c2f76d9587d6dd0399 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -308,7 +308,11 @@ string Bayesian::getTaxonomy(Sequence* seq) {
                //bootstrap - to set confidenceScore
                int numToSelect = queryKmers.size() / 8;
        
+        if (m->debug) {  m->mothurOut(seq->getName() + "\t"); }
+        
                tax = bootstrapResults(queryKmers, index, numToSelect);
+        
+        if (m->debug) {  m->mothurOut("\n"); }
                
                return tax;     
        }
@@ -374,6 +378,7 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                int seqTaxIndex = tax;
                TaxNode seqTax = phyloTree->get(tax);
                
+        
                while (seqTax.level != 0) { //while you are not at the root
                                        
                                itBoot2 = confidenceScores.find(seqTaxIndex); //is this a classification we already have a count on
@@ -383,11 +388,13 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                                        confidence = itBoot2->second;
                                }
                                
+                if (m->debug) { m->mothurOut(seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");"); }
+            
                                if (((confidence/(float)iters) * 100) >= confidenceThreshold) {
                                        confidenceTax = seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");" + confidenceTax;
                                        simpleTax = seqTax.name + ";" + simpleTax;
                                }
-                               
+            
                                seqTaxIndex = seqTax.parent;
                                seqTax = phyloTree->get(seqTax.parent);
                }