Issues
======
+ Solved 1
           

Complexity increasing per file
==============================
- pgatk/commands/cbioportal_downloader.py  6
- pgatk/commands/utils.py  5
- pgatk/commands/ensembl_downloader.py  25
- pgatk/commands/vcf_to_proteindb.py  19
- pgatk/commands/dnaseq_to_proteindb.py  13
- pgatk/commands/cosmic_downloader.py  4
- pgatk/db/map_peptide2genome.py  34
- pgatk/commands/ensembl_database.py  1
- pgatk/cgenomes/cosmic_downloader.py  16
- pgatk/commands/blast_get_position.py  4
- pgatk/ensembl/ensembl.py  149
- pgatk/cli.py  2
- pgatk/proteogenomics/spectrumai.py  57
- pgatk/commands/threeframe_translation.py  3
- pgatk/cgenomes/cbioportal_downloader.py  49
- pgatk/commands/proteindb_decoy.py  17
- pgatk/commands/cosmic_to_proteindb.py  8
- pgatk/db/digest_mutant_protein.py  27
- pgatk/proteogenomics/blast_get_position.py  35
- pgatk/commands/cbioportal_to_proteindb.py  9
- pgatk/proteomics/db/protein_database_decoy.py  78
- pgatk/ensembl/data_downloader.py  98
- pgatk/ensembl/exceptions.py  1
- pgatk/proteomics/models.py  1
- pgatk/cgenomes/cgenomes_proteindb.py  123
- pgatk/commands/validate_peptides.py  9
- pgatk/toolbox/general.py  68
- pgatk/config/registry.py  3
- pgatk/commands/digest_mutant_protein.py  1
- pgatk/commands/map_peptide2genome.py  1
- pgatk/commands/clinvar_to_proteindb.py  1
- pgatk/clinvar/clinvar_service.py  97
- pgatk/commands/ncbi_downloader.py  1
- pgatk/clinvar/chromosome_mapper.py  23
- pgatk/toolbox/vcf_utils.py  29
- pgatk/clinvar/data_downloader.py  16
         

Clones added
============
- pgatk/db/map_peptide2genome.py  2
- pgatk/cgenomes/cbioportal_downloader.py  2
- pgatk/commands/cosmic_to_proteindb.py  1
- pgatk/commands/cbioportal_to_proteindb.py  1
- pgatk/proteomics/db/protein_database_decoy.py  2
- pgatk/ensembl/data_downloader.py  8