major refactoring and update for all the providers. - #105

Issues
======
+ Solved 1
           

Complexity increasing per file
==============================
- pgatk/commands/ensembl_downloader.py  9
- pgatk/commands/vcf_to_proteindb.py  1
- pgatk/commands/cosmic_downloader.py  1
- pgatk/db/map_peptide2genome.py  2
- pgatk/cgenomes/cosmic_downloader.py  17
- pgatk/ensembl/ensembl.py  55
- pgatk/cgenomes/cbioportal_downloader.py  41
- pgatk/commands/cosmic_to_proteindb.py  1
- pgatk/db/digest_mutant_protein.py  2
- pgatk/commands/cbioportal_to_proteindb.py  8
- pgatk/ensembl/data_downloader.py  9
- pgatk/cgenomes/cgenomes_proteindb.py  130
- pgatk/toolbox/general.py  9
- pgatk/clinvar/clinvar_service.py  52
- pgatk/commands/ncbi_downloader.py  9
- pgatk/clinvar/data_downloader.py  16
- scripts/benchmark_vcf_to_proteindb.py  13
- pgatk/commands/gencode_downloader.py  4
- pgatk/commands/gnomad_vcf_downloader.py  5
- pgatk/gnomad/data_downloader.py  53
         

Clones added
============
- pgatk/ensembl/ensembl.py  2
- pgatk/commands/cosmic_to_proteindb.py  1
- pgatk/commands/cbioportal_to_proteindb.py  1
- pgatk/ensembl/data_downloader.py  3
- pgatk/clinvar/clinvar_service.py  2
- pgatk/clinvar/data_downloader.py  4
- pgatk/gnomad/data_downloader.py  2