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Supporting the genepred format. Required changes to existing BED code

Marek Szuba requested to merge feature/genepredbed into master

Created by: andrewyatz

Re-opening pull request #74 against master

This was some code to support the UCSC format extension to BED to support Gene predictions. Details of the format is here:

Some example data from here:

This data was GRCh37 data so you have to go back to release 76 or the 37 archive server to get the right data out. As far as I can tell we are doing the right thing. It also fixes a number of issues with incorrect phase representation. It seems the convention is to map them as -1 if they are non-coding and 0 if they are a starting coding exon. We seem to store these as -1 so that wasn't quite in sync with the way UCSC work.

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