fold halfWindowSize into args plumbing

[ryan-williams]

No description provided.

[coveralls]

Coverage increased (+0.09%) to 78.757% when pulling b855ea5 on ryan-williams:hws into 738996d on hammerlab:master.

[arahuja]

Looks fine to me, I don't necessarily see any advantages/disadvantages here - any background on that?

[ryan-williams]

Sure, sorry I didn't provide more context.

I'm diving back into some loci-partitioning stuff to explore sending only the necessary reference material to each partition, rather than Broadcasting it per-contig.

The halfWindowSize treatment through the loci-partitioning logic felt like it was not encapsulated correctly:

• one of the three loci-partitioners use it while the other two don't,
• all callers of loci-partitioning code except for GermlineAssemblyCaller set it to 0 without even offering a flag to configure it,
• yet it was being plumbed through as a top-level parameter in the LociPartitioner and PartitionedRegions APIs, and hard-coded to 0 in callers that don't care about it.

The API I'm trying to support for loci-partitioners is:

• everything specific to each partitioner gets passed to that partitioner as a ctor arg, and is hidden from the general LociPartitioner interface.
• things that are common to all partitioners can be part of the shared interface.
  • currently, that's just the LociSet => LociPartitioning shape.

Assembly callers want to map their --assembly-window-range parameter to the half-window-size, so I've done this by having CappedRegionsPartitionerArgs mix-in a halfWindowSize method that AssemblyArgs overrides and maps that flag to.

In a forthcoming PR I add a thin "partition-loci" top-level guac command that wants to do the same thing but with a different flag, so mixing-in and overriding HalfWindowConfig is a way to let multiple commands plumb half-windows through the loci-partitioning logic while allowing them to configure that value through CLI flags (or other logic) of their choice.

[coveralls]

Changes Unknown when pulling 10c595b on ryan-williams:hws into * on hammerlab:master*.