fixed sub.sample so that it will eliminate samples with abundances that are less...

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 5f522a659e0caf4adf63206ea280d9e130bdf8ae..7f0cd0a85ffded74edea865c2d2d9378d53d9dd8 100644 (file)
--- 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);
        }
 }