fixed bug with blastdb.cpp

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 97b331b65b556baafbd721cc6d0186097bdfa09e..5d714fd1ee88ff18a00619e96ae253847883a151 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -34,6 +34,7 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
                numWanted = numw;
                realign = r; 
                trimChimera = trim;
+               numNoParents = 0;
        
                doPrep();
        }
@@ -65,6 +66,7 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
                realign = r; 
                trimChimera = trim;
                priority = prior;
+               numNoParents = 0;
                
                createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
                
@@ -1115,6 +1117,8 @@ vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence q, vector<Sequence*>& db,
                //string qname = q->getName().substr(0, q->getName().find_last_of('_'));        
                //cout << qname << endl;        
                
+               if (mergedResults.size() == 0) { numNoParents++; }
+               
                for (int i = 0; i < mergedResults.size(); i++) {
                        //cout << q->getName() << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl; 
                        if (db[mergedResults[i]]->getName() != q.getName()) { 
@@ -1127,8 +1131,6 @@ vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence q, vector<Sequence*>& db,
                delete queryRight;
                delete queryLeft;
                
-               if (refResults.size() == 0) { m->mothurOut("[WARNING]: megablast returned 0 potential parents, so we are not able to check " + q.getName() + ". This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
-               
                return refResults;
        }
        catch(exception& e) {