rsem v1.1.12, add a script to extract transcript-to-gene-map info from Trinity output

[rsem.git] / Refs.h

diff --git a/Refs.h b/Refs.h
index 63b67e16e0d705d8c66d3946085f76b79496724c..67c5d57a349ab589a479b6ac0608058e86cb973e 100644 (file)
--- 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)));
   }