BESST
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Generate output patch
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