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Fixing the test suite and bits of io

Marek Szuba requested to merge bugfix/fixtestsuitev2 into master

Created by: andrewyatz

There's a few changes coming in here. Short summary

  • Tests will skip if you don't have Htslib/Kent XS bindings and core API. Tests always run on Travis no matter what
  • Expanding the cpanfile and install dependencies
  • Rejigged the big file parser
  • Removed the VEP_output parser. Will said it wasn't right to keep in
  • and the writer.t test now work. There's some awful delimiter initialisation problem that means I have to fake open a file

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