Remove PileupFilter and revamp InputFilters

[arahuja]

This PR:

• removes PileupFilter files and usage from SomaticStandard
• Add ReadFilterArgs which has flags to set properties of InputFilters
  • This includes moving around some of the arg traits to have LociArgs and ReadFilterArgs tied to read inputs hierarchy as opposed to partitioning.
  • Reaching way back - closes #135!
• Revamping some of InputFilters to tie in with arg-parsing and removing some defaults
  • Part of this includes having LociParser result in None when no loci are specified and removing the fallback arguments as sometimes this strings were incorrectly specified.
  • Another piece was removing the default InputFilters in a few cases. In https://github.com/hammerlab/guacamole/commit/3bcca667bd506a8eba5f85951f2856ccbe899f70 SomaticStandard went from removing duplicate and failed reads to including them because of a default filter argument, so I wanted to avoid that.

[coveralls]

Coverage increased (+0.5%) to 79.169% when pulling e27ba66219fa007776e723186c2532d408c4630f on read-filters into dfdfea6c9bda4040a7dd67decb862d9988b9c33c on master.

[ryan-williams]

Looks great, thanks for cleaning all this up.

While reviewing I was inspired to do a further loci-parsing refactor that I'd attempted and failed a few times in the past, but finally cracked this time: #606.

A couple small things in #606 are separable and more like bona-fide tweaks to what is here, but on the whole it's a separate PR and can be reviewed/merged as such.

I opened #606 against this in case you want to merge it in here, but if not you can just merge this and I'll send out #606 as a fresh PR.

[coveralls]

Coverage increased (+0.09%) to 78.745% when pulling c3831f4f2a1a9bfe4957cc6fa1530df340e05a53 on read-filters into dfdfea6c9bda4040a7dd67decb862d9988b9c33c on master.