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Attempting to fix the currently breaking test suite.

Closed Marek Szuba requested to merge bugfix/correctbrokenparsers into master

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.

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