chimera.slayer debugging

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index eb2b06e5c0229fd269631d8f642f00639025830c..1d22bdfe36f74194d2609c01b956cf0ab8ba67c8 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -217,7 +217,7 @@ int ChimeraSlayer::doPrep() {
                }else if (searchMethod == "blast") {
                
                        //generate blastdb
-                       databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
+                       databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3);
 
                        for (int i = 0; i < templateSeqs.size(); i++) {         databaseLeft->addSequence(*templateSeqs[i]);    }
                        databaseLeft->generateDB();
@@ -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;
                                        
@@ -782,7 +782,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                                realigner.reAlign(query, parents);
 
                        }
-
+                       
                        //get sequence that were given from maligner results
                        vector<SeqDist> seqs;
                        map<string, float> removeDups;
@@ -792,14 +792,20 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                        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
-                               itDup = removeDups.find(Results[j].parent);
-                               if (itDup == removeDups.end()) { //this is not duplicate
-                                       removeDups[Results[j].parent] = dist;
-                                       parentNameSeq[Results[j].parent] = Results[j].parentAligned;
-                               }else if (dist > itDup->second) { //is this a stronger number for this parent
-                                       removeDups[Results[j].parent] = dist;
-                                       parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+
+                               if(Results[j].queryToParentLocal >= 90){        //local match has to be over 90% similarity
+                               
+                                       itDup = removeDups.find(Results[j].parent);
+                                       if (itDup == removeDups.end()) { //this is not duplicate
+                                               removeDups[Results[j].parent] = dist;
+                                               parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+                                       }else if (dist > itDup->second) { //is this a stronger number for this parent
+                                               removeDups[Results[j].parent] = dist;
+                                               parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+                                       }
+                               
                                }
+                               
                        }
                        
                        for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
@@ -809,7 +815,6 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                                SeqDist member;
                                member.seq = seq;
                                member.dist = itDup->second;
-                               
                                seqs.push_back(member);
                        }
                        
@@ -827,8 +832,14 @@ 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 +1097,11 @@ 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;