added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index c8896375b016ef6c45462351a18e8e520bfe75c2..ef41ee1bab8853f6741938005f775076b60723ab 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -475,6 +475,9 @@ vector<string> ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* th
                                }
                                
                        }
+            
+            //phylotree adds an extra unknown so we want to remove that
+            if (bestChild.name == "unknown") { bestChildSize--; }
                                
                        //is this taxonomy above cutoff
                        int consensusConfidence = ceil((bestChildSize / (float) size) * 100);
@@ -541,7 +544,9 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                        taxaSum = new PhyloSummary(groupfile);
                }
                
+
                //for each bin in the list vector
+        string snumBins = toString(processList->getNumBins());
                for (int i = 0; i < processList->getNumBins(); i++) {
                        
                        if (m->control_pressed) { break; }
@@ -552,7 +557,15 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                        if (m->control_pressed) { out.close();  return 0; }
                        
                        //output to new names file
-                       out << (i+1) << '\t' << size << '\t' << conTax << endl;
+            string binLabel = "Otu";
+            string sbinNumber = toString(i+1);
+            if (sbinNumber.length() < snumBins.length()) { 
+                int diff = snumBins.length() - sbinNumber.length();
+                for (int h = 0; h < diff; h++) { binLabel += "0"; }
+            }
+            binLabel += sbinNumber;
+
+                       out << binLabel << '\t' << size << '\t' << conTax << endl;
                        
                        string noConfidenceConTax = conTax;
                        m->removeConfidences(noConfidenceConTax);