From: westcott <westcott>
Date: Thu, 23 Dec 2010 19:41:30 +0000 (+0000)
Subject: fixed memory leak in maligner minCoverageFilter function used by chimera slayer
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=f1e2f581f91d88e9d6c7a69e495b36031b29e4ab

fixed memory leak in maligner minCoverageFilter function used by chimera slayer
---

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 3497579..1336876 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -297,14 +297,14 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 		querySeq = query;
 		
 		//referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
-		maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
-		slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
+		Maligner maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
+		Slayer slayer(window, increment, minSim, divR, iters, minSNP);
 	
 		if (m->control_pressed) {  return 0;  }
 		
-		string chimeraFlag = maligner->getResults(query, decalc);
+		string chimeraFlag = maligner.getResults(query, decalc);
 		if (m->control_pressed) {  return 0;  }
-		vector<results> Results = maligner->getOutput();
+		vector<results> Results = maligner.getOutput();
 			
 		//found in testing realigning only made things worse
 		if (realign) {
@@ -381,16 +381,16 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 			if (m->control_pressed) {  for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }  return 0;  }
 			
 			//send to slayer
-			chimeraFlags = slayer->getResults(query, seqsForSlayer);
+			chimeraFlags = slayer.getResults(query, seqsForSlayer);
 			if (m->control_pressed) {  return 0;  }
-			chimeraResults = slayer->getOutput();
+			chimeraResults = slayer.getOutput();
 			
 			//free memory
 			for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }
 		}
 		
-		delete maligner;
-		delete slayer;
+		//delete maligner;
+		//delete slayer;
 		
 		return 0;
 	}
diff --git a/chimeraslayer.h b/chimeraslayer.h
index e4615ee..6d57474 100644
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -38,8 +38,6 @@ class ChimeraSlayer : public Chimera {
 	private:
 		Sequence* querySeq;
 		DeCalculator* decalc;
-		Maligner* maligner;
-		Slayer* slayer;
 		map<int, int>  spotMap;
 		Database* databaseRight;
 		Database* databaseLeft;
diff --git a/decalc.cpp b/decalc.cpp
index ff68ca5..8d90a78 100644
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -835,8 +835,6 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 			indexes.push_back(dists[i].index);
 		}
 		
-		dists.clear(); distsLeft.clear(); distsRight.clear();
-		
 		return seqsMatches;
 	}
 	catch(exception& e) {
diff --git a/maligner.cpp b/maligner.cpp
index 5f522a6..6deeb80 100644
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -178,6 +178,8 @@ vector<Sequence*> Maligner::minCoverageFilter(vector<Sequence*> ref){
 			//if coverage above minimum
 			if (coverage > minCoverage) {
 				newRefs.push_back(ref[i]);
+			}else {
+				delete ref[i];
 			}
 		}
 		
diff --git a/mothur b/mothur
index 6347591..2578194 100755
Binary files a/mothur and b/mothur differ