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Remove some old modules

Marek Szuba requested to merge github/fork/willmclaren/master into master

Created by: willmclaren

TranscriptSNPs and TranscriptAlleles were long ago superceded by modules in the ensembl-variation repo. The only other reference I can find was a use statement in the webcode which then makes no further reference to the method pulled in (I've put in a pull request to remove this too).

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