cancerit/VAGrENT: v3.3.0 - Re-write of the reference generation code

This release contains a complete replacement for the cache file generation code. Should make it function over a wider variety of Ensembl versions/species Decision tree for choosing which transcripts to include has changed The cache file format has not been changed If you regenerate an existing cache file with the new code base it will be compatible with older versions of VAGrENT but may not be identical. The set of transcripts included is quite likely to have changed