Develop#859
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The existing CLIs were out of date and untested. This commit introduces 3 new CLIs. variantvalidator, variantformatter and gene2transcripts. It removed batch_validator.py which is now covered by the variantvalidator CLI. It also removed a dangerous CLI which only deleted the VV database, and adds functionality to the vv_configuration CLI. All CLIs are tested and have help messages. The commit also restructures the VV logger setup so it can be overridden by interfaces without touching the config.ini
Update CLI and move code into VariantValidator
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