X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=5f522a659e0caf4adf63206ea280d9e130bdf8ae;hb=8af930b692ff87d1b7031fdd5c9a0b88cdd61245;hp=1d5258964650cad8c2e90d39414022e7dc2f0455;hpb=15cde0905641f8adddc1cc704f8c064f760e7461;p=mothur.git

diff --git a/maligner.cpp b/maligner.cpp
index 1d52589..5f522a6 100644
--- 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);