Fix fix of contigs + new orf sequence build

fixreference.py

@@ -208,8 +208,6 @@ def fix_contig(reference, protein, ref_seq, id_ref, id_prot, reverse, fixed_orf_
                 len_gap = len(item)
                 if len_gap >= GAP_BLOCK_SIZE_MIN:
                     gaps_block.append((position, position + (len_gap * 3), "ref"))
-                new_refseq += ref_seq[position: position + (len_gap * 3)]  # Remove this to remove gaps in new map
-                position += len_gap * 3
             elif re.match("^[A-Za-z*]+$", item) is not None:
                 if len(item) >= GAP_BLOCK_SIZE_MIN:
                     gaps_block.append((position, len(item), "prot"))
@@ -232,6 +230,7 @@ def fix_contig(reference, protein, ref_seq, id_ref, id_prot, reverse, fixed_orf_
 
     if reverse:  # Restore intial sequence
         new_refseq = str(Seq(new_refseq).reverse_complement())
+        ref_seq = str(Seq(ref_seq).reverse_complement())
 
     contig_seq = fasta.fetch(id_ref)
     fixed_contig = contig_seq.replace(ref_seq, new_refseq)