X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Refs.h;h=67c5d57a349ab589a479b6ac0608058e86cb973e;hb=791b978145b0d22865ee350db9d58072bb99d816;hp=63b67e16e0d705d8c66d3946085f76b79496724c;hpb=37513308b7557ae65899e59df8e43b5dec90da5c;p=rsem.git

diff --git a/Refs.h b/Refs.h
index 63b67e1..67c5d57 100644
--- a/Refs.h
+++ b/Refs.h
@@ -97,7 +97,10 @@ void Refs::makeRefs(char *inpF, RefSeqPolicy& policy, PolyARules& rules) {
     while((pt = getline(fin, line)) && line[0] != '>') {
       rawseq += line;
     }
-    assert(rawseq.size() > 0);
+    if (rawseq.size() <= 0) {
+      printf("Warning: Fasta entry %s has an empty sequence! It is omitted!\n", tag.c_str()); 
+      continue;
+    }
     ++M;
     seqs.push_back(RefSeq(tag, policy.convert(rawseq), rules.getLenAt(tag)));
   }