Add pigz and worker pool - #17
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Pull Request Overview
This PR adds support for pigz (parallel gzip) compression and introduces thread pool configuration. The changes allow the application to leverage pigz for faster compression/decompression when available, falling back to standard gzip otherwise. Additionally, thread count handling is improved by setting a default value of 1 when not specified.
Key Changes:
- Added pigz support with environment-based compression level configuration
- Introduced default thread count initialization
- Refactored gzip file handling into a dedicated method
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| src/heyfastqlib/command.py | Added default thread count initialization and removed pragma no cover comments |
| src/heyfastqlib/argparse_types.py | Implemented pigz support with fallback to gzip, refactored file opening logic, and fixed self.mode reference |
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…st-suite-and-relocate-tests Revamp test suite for pipelines and CLI
…tion-error-in-gzip-tests Fix pigz-backed GzipFileType text handling
…lines-multiprocessable-with-chunk-size Enable multiprocessing for read pipelines
…rror-in-subsample-command-test Fix subsample command to return stats
…bsample_reads-and-use-filter_reads Use filter_reads for subsampling
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