X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=cd268d3d6f1a513e932940332bab8ed15c59ada1;hb=1cf188b912d6da8f2cd03dd71cecef664a699c1a;hp=5868a7c721e69a9206a668536f35d02d573c9568;hpb=9489965363593bb2a3e94f801b4079a32ddf8732;p=mothur.git

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 5868a7c..cd268d3 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -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;
@@ -993,7 +999,7 @@ 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
@@ -1019,12 +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;
 		
@@ -1037,7 +1043,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
 		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()) {  
@@ -1065,7 +1071,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
 		}
 
 		for (int i = 0; i < mergedResults.size(); i++) {
-			
+			//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);