added kmer stuff

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index a182b846cc4f84288e029188f53c25dcf4ea93cc..efd29d64035e390c7b48aba87f3b93fdd8c1eb68 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -1150,17 +1150,44 @@ vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db,
                //merge results         
                map<int, int> seen;
                map<int, int>::iterator it;
-                       vector<int> mergedResults;
-               for (int i = 0; i < tempIndexesLeft.size(); i++) {
+               vector<int> mergedResults;
+               
+               int index = 0;
+               //              for (int i = 0; i < smaller.size(); i++) {
+               while(index < tempIndexesLeft.size() && index < tempIndexesRight.size()){
                        
                        if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
                        
                        //add left if you havent already
+                       it = seen.find(tempIndexesLeft[index]);
+                       if (it == seen.end()) {  
+                               mergedResults.push_back(tempIndexesLeft[index]);
+                               seen[tempIndexesLeft[index]] = tempIndexesLeft[index];
+                       }
+                       
+                       //add right if you havent already
+                       it = seen.find(tempIndexesRight[index]);
+                       if (it == seen.end()) {  
+                               mergedResults.push_back(tempIndexesRight[index]);
+                               seen[tempIndexesRight[index]] = tempIndexesRight[index];
+                       }
+                       index++;
+               }
+               
+               
+               for (int i = index; i < tempIndexesLeft.size(); i++) {
+                       if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+                       
+                       //add right if you havent already
                        it = seen.find(tempIndexesLeft[i]);
                        if (it == seen.end()) {  
                                mergedResults.push_back(tempIndexesLeft[i]);
                                seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
                        }
+               }
+               
+               for (int i = index; i < tempIndexesRight.size(); i++) {
+                       if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
                        
                        //add right if you havent already
                        it = seen.find(tempIndexesRight[i]);
@@ -1170,17 +1197,16 @@ vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db,
                        }
                }
                
-               //numWanted = mergedResults.size();
-                       
-               //cout << q->getName() << endl;         
                
                for (int i = 0; i < mergedResults.size(); i++) {
-                       //cout << db[mergedResults[i]]->getName() << endl;      
+                       //cout << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl; 
                        if (db[mergedResults[i]]->getName() != q->getName()) { 
                                Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
                                refResults.push_back(temp);
+                               
                        }
                }
+
                //cout << endl;         
                delete queryRight;
                delete queryLeft;