Bug-fix iteration: closes #98, #99, #100, #101 #102

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Open

ypriverol wants to merge 24 commits into dev from feat/bug-fixed-iteration

Open

Bug-fix iteration: closes #98, #99, #100, #101 #102

Merge pull request #104 from bigbio/perf/vcf-to-proteindb-parallel

Codacy Production / Codacy Static Code Analysis required action May 14, 2026 in 0s

39 new issues (0 max.) of at least severity.

Here is an overview of what got changed by this pull request:

Issues
======
- Added 39
           

Complexity increasing per file
==============================
- pgatk/commands/vcf_to_proteindb.py  1
- pgatk/commands/cosmic_downloader.py  1
- pgatk/cgenomes/cosmic_downloader.py  17
- pgatk/ensembl/ensembl.py  40
- pgatk/commands/cosmic_to_proteindb.py  1
- pgatk/cgenomes/cgenomes_proteindb.py  24
- pgatk/tests/pgatk_tests.py  24
- pgatk/tests/test_cosmic_downloader.py  2
- scripts/benchmark_vcf_to_proteindb.py  13
- pgatk/tests/test_variant_types_hgvs.py  21
- pgatk/tests/test_vcf_to_proteindb_parallel.py  9
         

Clones added
============
- pgatk/commands/cosmic_to_proteindb.py  1

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