Coordinates for bed files should be 0 based, while gff is 1 based

[blakesweeney]

UCSC and ENSEMBL both define bed files as being 0 based:

https://genome.ucsc.edu/FAQ/FAQformat.html#format1 http://www.ensembl.org/info/website/upload/bed.html

while gff files are 1 based:

https://genome.ucsc.edu/FAQ/FAQformat.html#format3 http://www.ensembl.org/info/website/upload/gff.html

currently we export both files (at least for pome) as 1 based.