Support for regular varcode variant instances in read evidence module

[timodonnell]

The read evidence module has been in an awkward place since it uses a different Variant class than the rest of varcode, as it uses interbase coordinates whereas the rest of varcode uses 1-based coordinates. (Varcode will eventually migrate entirely to interbase; see #40). This change makes this situation mildly less annoying by having the read evidence module take care of converting regular varcode Variant instances to the needed interase format.

[timodonnell]

Mind taking a quick perusal of this, @tavinathanson ?

[tavinathanson]

Nit: maybe mark this with TODO for easy discovery of TODOs (I should probably put this suggestion in the wiki)

[tavinathanson]

@timodonnell I'm somewhat confused by the read_evidence module; for starters, I don't see your version of Variant defined anywhere, or for that matter, code that actually uses the read_evidence module.

Update: Ah, I'm now looking at https://github.com/hammerlab/ovarian-cancer/blob/53c92e7ddc0b81b0864c7d28fd112c75c8747472/projects/pt189/read_evidence_plot.py to get a feel for usage.

[tavinathanson]

I'm confused about why variant and locus are combined here?

(In general, I feel like x_or_y isn't good practice, but I don't yet understand why the code wants this in the first place.)