- if entry1 and entry2
- merged = Assemble.pair(
- entry1,
- entry2,
- mismatches_max:options[:mismatches],
- overlap_min:options[:overlap_min],
- overlap_max:options[:overlap_max]
- )
-
- if merged
- new_record = merged.to_bp
-
- if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
- new_record[:OVERLAP] = $1
- new_record[:HAMMING_DIST] = $2
- end
+ if entry1 and
+ entry2 and
+ entry1.length >= options[:overlap_min] and
+ entry2.length >= options[:overlap_min]
+
+ if names_match(entry1, entry2)
+ entry2.type = :dna
+ entry2.reverse!.complement!
+
+ merged = Assemble.pair(
+ entry1,
+ entry2,
+ mismatches_max:options[:mismatches],
+ overlap_min:options[:overlap_min],
+ overlap_max:options[:overlap_max]
+ )