jamescasbon/PyVCF — pull request #160 by gotgenes (2014-05-19 06:45:41+00:00)
Title: Fixes _Record.start and .end to reflect affected region.

`_Record.start` and `_Record.end` should represent the zero-based, half-open region of the contig affected by all the events included in ALT, so that the user can correctly identify the range of the region affected by the record.

Prior to this, the code correctly indicated the region of the reference affected only for the case of SNVs and structural variants. For all other types of variants, the coordinates were incorrect, including the beginning base from `REF` that is there simply as the contextual base before the event per VCF specifications.

I think a good deal of this code should be pushed down to the individual `ALT` classes but this is a discussion for another day. For now, this patch will at least enable users to correctly determine overlap of the record with a portion of the reference genome.