Consolidate ReferenceRegion, Position, etc.

[fnothaft]

We had discussed this a bit on another thread; this winds up being a consolidation of #511, #517, #592, Here's what I propose:

1. Eliminate ReferencePosition. A ReferencePosition is just a special case of a ReferenceRegion (region with width = 1). For the cost of 1 Long field, we could eliminate a lot of duplicated code.
2. Eliminate the *WithOrientation models. We have a Strand enum: https://github.com/bigdatagenomics/bdg-formats/blob/master/src/main/resources/avro/bdg.avdl#L720.
3. Move ReferenceRegion to Avro. This will allow us to consolidate fields in AlignmentRecord, Variant, and NucleotideContigFragment. I think we'd keep the org.bdgenomics.adam.models.ReferenceRegion object, and consolidate an apply method, as well as the overlaps, isAdjacent, etc methods there.
4. As proposed in ReferenceRegion shouldn't extend Ordered #511, add an Ordering for ReferenceRegion.

[tdanford]

+1 on the first two points, and the fourth. Need to think about the third?

[tdanford]

Will this really allow us to consolidate AlignmentRecord, Variant, etc?

Wouldn't the ideal be that those (generated) classes all inherit from a common ReferenceRegion superclass? Is that possible with Avro?

(Isn't this what sparked our discussion of Thrift on the call a week or two ago?)

[fnothaft]

I don't think it'd be ideal to have them inherit from a common class, because they all have different implementations. E.g., variants have a single required mapping. Reads (in the fragment model, which I prefer) have multiple optional mappings. Contigs have a single optional mapping.

[fnothaft]

I'll open a PR against bdg-formats showing what I'm talking about.

[tdanford]

That'd be great.

[laserson]

I agree with @tdanford. Bullet 3 seems like a more complex issue, which I'm more ok to punt on at the moment. I agree that there are advantages to having a non-Avro ReferenceRegion, so would it be confusing to also have an Avro ReferenceRegion?

[tdanford]

Frank, can you rewrite the issue description above to use a number list rather than bullets? :-)

[fnothaft]

Frank, can you rewrite the issue description above to use a number list rather than bullets? :-)

Fixed!

[fnothaft]

Closed via #624.