Mark DePristo comments

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                                            Mark DePristo

happy treats variants that aren't fully within the confident regions as confident

Here's a concrete example: ``` candidate: no call is present truth: 20 16755600 rs369843912 AAGAAAAAAG A 50 PASS . GT:DP:ADALL:AD:GQ:IGT:IPS:PS 0/1:228:130,71:145,77:366:0/1:.:. happy: 20 16755600 . AAGAAAAAAG A 50 . BS=16755600;Regions=CONF,TS_contained...

Pass data objects into ggplot call

sirrice, btw, I'm going to handle all of these open issues. Just put them here for proper bookkeeping

Pass data objects into ggplot call

Oops, didn't realize this was a distinct issue. Happy if you want to handle this one.