continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due...

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 958f29b39213c3fda29e810af8832fef4afa83e1..da807bdd5103e5f8f8024217e12b15e4ba1b59ce 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -272,6 +272,11 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                for(int i=0;i<line->numSeqs;i++){
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);
+
+                       if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
+                               alignment->resize(candidateSeq->getUnaligned().length()+1);
+                       }
+                       
                        report.setCandidate(candidateSeq);
        
                        Sequence temp = templateDB->findClosestSequence(candidateSeq);