chimera.slayer fix

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 1d5258964650cad8c2e90d39414022e7dc2f0455..5f522a659e0caf4adf63206ea280d9e130bdf8ae 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);