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perf(vcf-to-proteindb): per-chromosome multiprocessing (~3.4× on 4-chrom test) #104

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Merged
ypriverol merged 4 commits into from
May 14, 2026

Revert non-deterministic test output; gitignore SeqIO.index_db files

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Merged

perf(vcf-to-proteindb): per-chromosome multiprocessing (~3.4× on 4-chrom test) #104

Revert non-deterministic test output; gitignore SeqIO.index_db files
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Codacy Production / Codacy Static Code Analysis required action May 13, 2026 in 0s

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

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

Issues
======
- Added 3
           

Complexity increasing per file
==============================
- pgatk/commands/vcf_to_proteindb.py  1
- pgatk/ensembl/ensembl.py  27
- scripts/benchmark_vcf_to_proteindb.py  8
- pgatk/tests/test_vcf_to_proteindb_parallel.py  9

See the complete overview on Codacy

Annotations

Check warning on line 55 in pgatk/tests/test_vcf_to_proteindb_parallel.py

See this annotation in the file changed.

@codacy-production codacy-production / Codacy Static Code Analysis

pgatk/tests/test_vcf_to_proteindb_parallel.py#L55 

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.

Check warning on line 58 in pgatk/tests/test_vcf_to_proteindb_parallel.py

See this annotation in the file changed.

@codacy-production codacy-production / Codacy Static Code Analysis

pgatk/tests/test_vcf_to_proteindb_parallel.py#L58 

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.

Check warning on line 64 in pgatk/tests/test_vcf_to_proteindb_parallel.py

See this annotation in the file changed.

@codacy-production codacy-production / Codacy Static Code Analysis

pgatk/tests/test_vcf_to_proteindb_parallel.py#L64 

Use of assert detected. The enclosed code will be removed when compiling to optimised byte code.
View more details on Codacy Production