X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=7f0cd0a85ffded74edea865c2d2d9378d53d9dd8;hb=92de7f976371d41441ad41f02ca83af8b43cef5c;hp=5f522a659e0caf4adf63206ea280d9e130bdf8ae;hpb=8af930b692ff87d1b7031fdd5c9a0b88cdd61245;p=mothur.git

diff --git a/maligner.cpp b/maligner.cpp
index 5f522a6..7f0cd0a 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];
 			}
 		}
 		
@@ -549,9 +551,9 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 		}
 		
 		if (mergedResults.size() < numWanted) { numWanted = mergedResults.size(); }
-//cout << q->getName() <<  endl;		
+//cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted <<  endl;		
 		for (int i = 0; i < numWanted; i++) {
-//cout << db[mergedResults[i]]->getName() << endl;	
+//cout << db[mergedResults[i]]->getName()  << '\t' << mergedResults[i] << endl;	
 			if (db[mergedResults[i]]->getName() != q->getName()) { 
 				Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
 				refResults.push_back(temp);
@@ -559,7 +561,7 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 			}
 //cout << mergedResults[i] << endl;
 		}
-//cout << endl;		
+//cout << "done " << q->getName()  << endl;		
 		delete queryRight;
 		delete queryLeft;
 			
@@ -622,7 +624,7 @@ vector<Sequence*> Maligner::getKmerSeqs(Sequence* q, int num) {
 		return refResults;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "Maligner", "getBlastSeqs");
+		m->errorOut(e, "Maligner", "getKmerSeqs");
 		exit(1);
 	}
 }