Sequence::value_type motif_char;
Sequence::value_type seq_char;
- while (seq_i < seq->length())
+ while (seq_i < size())
{
// this is pretty much a straight translation of Nora's python code
// to match iupac letter codes
motif_char = toupper(a_motif[motif_i]);
- seq_char = toupper(seq->at(seq_i));
+ seq_char = toupper(seq->at(seq_start+seq_i));
if (motif_char =='N')
motif_i++;
else if (motif_char == seq_char)