conversion between 0-based and 1-based coordinate systems

[rhdolin]

Prerequisites

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• [ x] I am running the latest version
• [ x] I checked the documentation and found no answer
• [x ] I checked to make sure that this issue has not already been filed

Context

BED files are 0-based, VCF files are 1-based. We need to make sure that we are converting correctly.

In the sequence 'AGCA', a 1-based 1..3 = AGC, whereas a 0-based 1..3 = GC.
If 1-based coordinates are 1..3, the corresponding 0-based coordinates are 0..3.