move strand into seqspan

[mussa.git] / alg / flp_seqcomp.cpp

diff --git a/alg/flp_seqcomp.cpp b/alg/flp_seqcomp.cpp
index f46c40498d58b4e12025deda0b293e3d0ee60acb..995a228ede7cc203a6a6c60a80342d8d2667e419 100644 (file)
--- a/alg/flp_seqcomp.cpp
+++ b/alg/flp_seqcomp.cpp
@@ -61,8 +61,10 @@ FLPs::seqcomp(const Sequence& sseq1, const Sequence& sseq2, bool is_RC)
   int start_i, seq1_i, seq2_i, win_i;      // loop variables
   int matches;                    // number of matches in to a window
   int i2_offset;
-  const char *seq1 = sseq1.c_str();
-  const char *seq2 = sseq2.c_str();
+  std::string sseq1_str(sseq1.get_sequence());
+  std::string sseq2_str(sseq2.get_sequence());
+  const char *seq1 = sseq1_str.c_str();
+  const char *seq2 = sseq2_str.c_str();
 
   validate_sequence(sseq1);
   validate_sequence(sseq2);