ryan-williams
commented
7 years ago 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
0without 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
0in 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 => LociPartitioningshape.
- currently, that's just the
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
Coverage increased (+0.09%) to 78.757% when pulling b855ea5568b109aa312e38ee26ae058823875ea3 on ryan-williams:hws into 738996d8cfcc4bbcabf2138cf269b965dff5b190 on hammerlab:master.