more chimera.slayer debugging

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index efd29d64035e390c7b48aba87f3b93fdd8c1eb68..423f7c0e713eef53a8904c2dcaff49a35844f35f 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -785,6 +785,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 
                        }
                        
+//                     cout << query->getAligned() << endl;
                        //get sequence that were given from maligner results
                        vector<SeqDist> seqs;
                        map<string, float> removeDups;
@@ -792,9 +793,12 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                        map<string, string> parentNameSeq;
                        map<string, string>::iterator itSeq;
                        for (int j = 0; j < Results.size(); j++) {
+
                                float dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal;
                                //only add if you are not a duplicate
-
+//                             cout << Results[j].parent << '\t' << Results[j].regionEnd << '\t' << Results[j].regionStart << '\t' << Results[j].regionEnd - Results[j].regionStart +1 << '\t' << Results[j].queryToParentLocal << '\t' << dist << endl;
+                               
+                               
                                if(Results[j].queryToParentLocal >= 90){        //local match has to be over 90% similarity
                                
                                        itDup = removeDups.find(Results[j].parent);
@@ -840,7 +844,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                        for (int k = 0; k < seqs.size(); k++) {  
 //                             cout << seqs[k].seq->getAligned() << endl;
                                seqsForSlayer.push_back(seqs[k].seq);   
-                       
+//                             cout << seqs[k].seq->getName() << endl;
                        }
                        
                        if (m->control_pressed) {  for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }  return 0;  }