Added first iteration of PhasedPanelEvaluation with PanGeniePanelCreation and refactored phasing pipeline.

[samuelklee]

Closes #4.
Closes #5.

This gets us most of the way through #1. See TODOs added there.

See a complete HPRC-only run evaluating over HG002 here: https://app.terra.bio/#workspaces/broad-firecloud-dsde/lrma-aou1-panel-creation-hprc-only/job_history/8c9cd513-ce20-479b-9fde-7e48adf5c374

This roughly automatically replicates the last slide of this deck (which was run manually for AoU+HPRC): https://docs.google.com/presentation/d/1jwCQCQo8_Nrwre-dQASmeSmsyhD9DjMASe4LMgfQ3uQ/edit?usp=sharing We see pretty much all of the same patterns, although the numbers slightly differ.

Note that the drop in recall in the last VCF (produced by PanGeniePanelCreation) is a good enough indicator of remaining overlap issues now (since the PanGenie script removes an entire allele if it is found to overlap in any one sample).

Both vcfdist and phasing pipelines were cleaned up (mostly for style) and renamed/moved. Probably could do with another round or two.

[samuelklee]

@hangsuUNC I am going to go ahead and merge this, but you might be interested in taking a look.