fixed bug with realigner for chimera slayer

[mothur.git] / slayer.cpp

diff --git a/slayer.cpp b/slayer.cpp
index 0ef795309a3f758c4f20e47e2e7504386aeaeb80..5ecb4ea7c5c430b34efc934b1e736915f363438c 100644 (file)
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -28,24 +28,18 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                                Sequence* q = new Sequence(query->getName(), query->getAligned());
                                Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned());
                                Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned());
-               //cout << "parents: (" << refSeqs[i]->getName() << ", " << refSeqs[j]->getName() << ")\n";
+       
                                map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
                                vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
-                               //cout << divs.size() << endl;
-                               if (m->control_pressed) { 
-                                       delete q;
-                                       delete leftParent;
-                                       delete rightParent;
-                                       return "no"; 
-                               }
+       
+                               if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
                                        
-//                             cout << divs.size() << endl;
                                vector<data_struct> selectedDivs;
                                for (int k = 0; k < divs.size(); k++) {
                                        
                                        vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
                                        vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
-                                       //cout << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << '\t' << k << divs[k].parentA.getAligned() << endl << divs[k].parentB.getAligned() << endl;  
+       
                                        if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
                                        
                                        int numSNPSLeft = snpsLeft.size();