Bigbed to gtf converter and tests

[d-callan]

adding a bigbed to gtf datatype converter. see galaxyproject/brc-analytics#371

leaned on the bed to gff converter a bit, for the sake of consistent treatment of similar things etc. let me know if we prefer a different strategy.

How to test the changes?

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• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
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[mvdbeek]

Is there a reason you're not using genePredToGtf ? I don't know if we can trust that 17 year old hand-written bed to gff script ...

[d-callan]

i was partly trying to be consistent w what was already here. it seemed to me like itd be unexpected as a user if i got a very different gtf vs gff2 file w the same input. but also, i was a little worried that if the incoming file wasnt from ucsc that the genepred intermediate file wouldnt make sense or maybe even work. (im not really confident i know what genepred is tbh) and if we did know the incoming data was from ucsc, why not have a genepred to gtf converter?

[mvdbeek]

Agree these are issues, but realistically I think all bigbeds come from ucsc. That said, I think the bigbed to bed converter was the important one that would have an application, maybe we can wait until there's a reason not to use the pre-built gtfs hosted by ucsc before we proceed here ? If there is an actual application we'll also know if this will all work out correctly.