X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Refs.h;h=67c5d57a349ab589a479b6ac0608058e86cb973e;hb=791b978145b0d22865ee350db9d58072bb99d816;hp=f411622f0cfb74c974db580e8e16091f1503d16d;hpb=3ec78aa9af79921c44d62b65f88865a4b65880be;p=rsem.git

diff --git a/Refs.h b/Refs.h
index f411622..67c5d57 100644
--- a/Refs.h
+++ b/Refs.h
@@ -52,7 +52,7 @@ class Refs {
   }
 
   bool isValid(int sid, int dir, int pos, const std::string& readseq, int LEN, int C) {
-    if (sid <= 0 || sid > M || dir != 0 && dir != 1 ||  pos < 0 || pos + LEN > seqs[sid].getTotLen() || LEN > (int)readseq.length()) return false;
+    if (sid <= 0 || sid > M || (dir != 0 && dir != 1) ||  pos < 0 || pos + LEN > seqs[sid].getTotLen() || LEN > (int)readseq.length()) return false;
     const std::string& seq = seqs[sid].getSeq(dir);
     return countMismatch(seq, pos, readseq, LEN, C) <= C;
   }
@@ -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)));
   }