Attempting to fix the currently breaking test suite.
Created by: andrewyatz
THIS CANNOT BE MERGED IN YET. DO NOT MERGE
This branch is a set of changes to master to make sure the test suite runs once again. Already there have been some hidden bugs (seek() in BigWig not -1 from the given start position) and removal of scripts masquerading as test cases.
There are still some issues with the VEP output code. From what I have seen the input file lacks the following columns
- consequence
- impact
- exon
- intron
- hgvsc
- hgvsp
Are these actually fields in the VEP output or do they come from the final attributes set? Either the input file needs changing or the VEP_output.pm parser needs changing.