Naming of "contig" module and type

[holtgrewe]

I think the contig module and Contig struct have a naming issue. From my understanding, "contig" is a well-established term from genome assembly that describes a contiguously assembled sequence. This is, e.g., supported by the contig header in VCF... Also, I believe genome::AbstractInterval::contig shares the description.

What about renaming this as "linear"?

[dlaehnemann]

I agree. I stumbled upon this naming during the rust-bio Docathon in some code using the Contig. What is described as a contig in contig.rs is rather an interval on some reference sequence (and this reference sequence could more aptly be referred to as a contig...). The Contig struct does not include the sequence itself.

So it should definitely get a clearer name. What about stranded_contig_interval? A bit long, but it captures all the properties. Or maybe just contig_interval?