BED Co-ordinates Off-by-1 bug

[nathanhaigh]

I noticed while looking at the BED file, in IGV, generated by Pilon that the left co-ordinate is off-by-1, at least for SNPs/indel features. Here are a few examples:

Deletion:

Insertion:

SNP:

[nathanhaigh]

BED co-ordinates are 0-based, half-open.

This blog post may help: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/