some minor changes

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 1d5258964650cad8c2e90d39414022e7dc2f0455..30e993678a92895146ac289f132ab9dc2f7ac73b 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -71,6 +71,9 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                
                //trims seqs to first non gap char in all seqs and last non gap char in all seqs
                spotMap = decalc->trimSeqs(query, refSeqs);
+               
+               //you trimmed the whole sequence, skip
+               if (query->getAligned() == "") { return "no"; }
 
                vector<Sequence*> temp = refSeqs;
                temp.push_back(query);
@@ -175,6 +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];
                        }
                }
                
@@ -619,7 +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);
        }
 }