tracking down chimera.slayer issue

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 4a00c1d47709d2137a2f79e875367b55bde1ed95..7d7145f4ca6bd9fac7a316745ace4432e4c26fe0 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -106,7 +106,7 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
 //             }
                
                if (trace.size() > 1) {         chimera = "yes";        }
-               else { chimera = "no";  }
+               else { chimera = "no";  return chimera; }
                
                int traceStart = trace[0].col;
                int traceEnd = trace[trace.size()-1].oldCol;    
@@ -727,17 +727,19 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
                        lasti++;                        
                }
                
-               numWanted = seen.size();
+               numWanted = mergedResults.size();
                
                if (mergedResults.size() < numWanted) { numWanted = mergedResults.size(); }
 //cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted <<  endl;           
                for (int i = 0; i < numWanted; i++) {
 //cout << db[mergedResults[i]]->getName()  << '\t' << mergedResults[i] << endl;        
+                       
                        if (db[mergedResults[i]]->getName() != q->getName()) { 
                                Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
                                refResults.push_back(temp);
                                indexes.push_back(mergedResults[i]);
                        }
+                       
 //cout << mergedResults[i] << endl;
                }
 //cout << "done " << q->getName()  << endl;