chimera.slayer debugging

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 73c61de4ea5ec66ca2d1d19f9ec2f1a9b01ed838..826f38ba962681e883809c5dcb2711939d205c99 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -552,7 +552,7 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef
                                if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS))  { leftChimeric = true;  } }
                                
                                if (rightChimeric || leftChimeric) {
-                                       cout << querySeq->getName() <<  "\tyes" << endl;
+//                                     cout << querySeq->getName() <<  "\tyes" << endl;
                                        outAccString += querySeq->getName() + "\n";
                                        results = true;
                                        
@@ -827,8 +827,14 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                        }
                
                        //put seqs into vector to send to slayer
+                       
+//                     cout << query->getAligned() << endl;
                        vector<Sequence*> seqsForSlayer;
-                       for (int k = 0; k < seqs.size(); k++) {  seqsForSlayer.push_back(seqs[k].seq);  }
+                       for (int k = 0; k < seqs.size(); k++) {  
+//                             cout << seqs[k].seq->getAligned() << endl;
+                               seqsForSlayer.push_back(seqs[k].seq);   
+                       
+                       }
                        
                        if (m->control_pressed) {  for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }  return 0;  }
 
@@ -1086,6 +1092,11 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                                
                        }
                }
+               
+               
+//             for(int i=0;i<refResults.size();i++){
+//                     cout << refResults[i]->getName() << endl;
+//             }
                        
                delete queryRight;
                delete queryLeft;