changes for chimera slayer

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index fe63ad0a9696cddc6ea1699bdc77922ef4f055c2..cd268d3d6f1a513e932940332bab8ed15c59ada1 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -103,8 +103,8 @@ int ChimeraSlayer::doPrep() {
                                if (m->control_pressed) {  return 0; }
                                
                                Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
-                               filteredTemplateSeqs.push_back(newSeq);
                                runFilter(newSeq);  
+                               filteredTemplateSeqs.push_back(newSeq);
                        }
                }
                string  kmerDBNameLeft;
@@ -743,7 +743,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                
                //moved this out of maligner - 4/29/11
                vector<Sequence*> refSeqs = getRefSeqs(query, thisTemplate, thisFilteredTemplate);
-                       
+               
                Maligner maligner(refSeqs, match, misMatch, divR, minSim, minCov); 
                Slayer slayer(window, increment, minSim, divR, iters, minSNP, minBS);
                
@@ -755,7 +755,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                if (m->control_pressed) {  return 0;  }
 
                string chimeraFlag = maligner.getResults(query, decalc);
-               
+
                if (m->control_pressed) {  return 0;  }
                
                vector<results> Results = maligner.getOutput();
@@ -763,12 +763,18 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                for (int i = 0; i < refSeqs.size(); i++) {  delete refSeqs[i];  }
                
                if (chimeraFlag == "yes") {
-                       
+
                        if (realign) {
-                               ChimeraReAligner realigner(thisTemplate, match, misMatch);
-                               realigner.reAlign(query, Results);
+                               vector<string> parents;
+                               for (int i = 0; i < Results.size(); i++) {
+                                       parents.push_back(Results[i].parentAligned);
+                               }
+                               
+                               ChimeraReAligner realigner;             
+                               realigner.reAlign(query, parents);
+
                        }
-                       
+
                        //get sequence that were given from maligner results
                        vector<SeqDist> seqs;
                        map<string, float> removeDups;
@@ -811,7 +817,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                                        seqs.pop_back();        
                                }
                        }
-                       
+               
                        //put seqs into vector to send to slayer
                        vector<Sequence*> seqsForSlayer;
                        for (int k = 0; k < seqs.size(); k++) {  seqsForSlayer.push_back(seqs[k].seq);  }
@@ -993,7 +999,8 @@ vector<Sequence*> ChimeraSlayer::getRefSeqs(Sequence* q, vector<Sequence*>& this
                        //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
                        Sequence* newSeq = new Sequence(q->getName(), q->getAligned());
                        runFilter(newSeq);
-                       refSeqs = decalc->findClosest(newSeq, thisTemplate, thisFilteredTemplate, numWanted);
+                       refSeqs = decalc->findClosest(newSeq, thisTemplate, thisFilteredTemplate, numWanted, minSim);
+                       delete newSeq;
                }else if (searchMethod == "blast")  {
                        refSeqs = getBlastSeqs(q, thisTemplate, numWanted); //fills indexes
                }else if (searchMethod == "kmer") {
@@ -1018,12 +1025,12 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
                string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
                
-               Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
-               Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
-               
-               vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
-               vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
+               Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
+               Sequence* queryRight = new Sequence(q->getName(), rightQuery);
                
+               vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1, minSim);
+               vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1, minSim);
+               cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery   << " rightMatches = " << tempIndexesRight.size() << endl;
                vector<int> smaller;
                vector<int> larger;
                
@@ -1035,6 +1042,8 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                map<int, int>::iterator it;
                vector<int> mergedResults;
                for (int i = 0; i < smaller.size(); i++) {
+                       if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+       
                        //add left if you havent already
                        it = seen.find(smaller[i]);
                        if (it == seen.end()) {  
@@ -1051,6 +1060,8 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                }
                
                for (int i = smaller.size(); i < larger.size(); i++) {
+                       if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+                       
                        //add right if you havent already
                        it = seen.find(larger[i]);
                        if (it == seen.end()) {  
@@ -1058,21 +1069,16 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                                seen[larger[i]] = larger[i];
                        }
                }
-               //numWanted = mergedResults.size();
 
-               //cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted <<  endl;            
                for (int i = 0; i < mergedResults.size(); i++) {
-                       //cout << db[mergedResults[i]]->getName()  << '\t' << mergedResults[i] << 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 << db[mergedResults[i]]->getName() << endl;
+                               
                        }
-                       
-                       //cout << mergedResults[i] << endl;
                }
-               //cout << "done " << q->getName()  << endl;             
+                       
                delete queryRight;
                delete queryLeft;
                
@@ -1086,6 +1092,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
 //***************************************************************************************************************
 vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db, int num) {
        try {   
+               vector<Sequence*> refResults;
                
                //get parts of query
                string queryUnAligned = q->getUnaligned();
@@ -1095,14 +1102,17 @@ vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db,
                Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
                Sequence* queryRight = new Sequence(q->getName(), rightQuery);
                
-               vector<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, numWanted);
-               vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, numWanted);
+               vector<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, num);
+               vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, num);
                
                //merge results         
                map<int, int> seen;
                map<int, int>::iterator it;
                        vector<int> mergedResults;
                for (int i = 0; i < tempIndexesLeft.size(); i++) {
+                       
+                       if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+                       
                        //add left if you havent already
                        it = seen.find(tempIndexesLeft[i]);
                        if (it == seen.end()) {  
@@ -1121,7 +1131,7 @@ vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db,
                //numWanted = mergedResults.size();
                        
                //cout << q->getName() << endl;         
-               vector<Sequence*> refResults;
+               
                for (int i = 0; i < mergedResults.size(); i++) {
                        //cout << db[mergedResults[i]]->getName() << endl;      
                        if (db[mergedResults[i]]->getName() != q->getName()) {