Here is the patch for output as describe in issue #55
As mentionned it's a big changed.

• check_kmer_overlap has been renamed compute_kmer_overlap as you suggested. I placed it outside Scaffold class.
• I had some tool classes : Component, Contig, and Gap. I think they can help code reading.
• Scaffold does not compute gaps,positions,directions, ... as list. The main computation (those list construction and the N integration, previously in make_fasta) has been placed in __buildComponents
• Those changes make output generation quite easy to understand I think. I place a description of rows for AGP and GFF in docstring comment.

I checked on my assembly that fasta output has not been altered.

I also made a unittest branch which I'll proposed to add to your repository in another pull request.
Sébastien