feat: parse samtools regions #40
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes introduce a new parameter, Changes
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
snakemake_wrapper_utils/samtools.py (1)
15-15: Update docstring to document the new parameter.The new
parse_regionsparameter should be documented in the function's docstring to maintain consistency with other parameters.
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snakemake_wrapper_utils/samtools.py (1)
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🔇 Additional comments (2)
snakemake_wrapper_utils/samtools.py (2)
52-62: LGTM! Implementation follows established patterns.
The regions file parsing block is well-implemented:
- Consistent error handling with other blocks
- Proper validation of both
--region-fileand--regions-filevariants - Clear error messages
- Follows the file's established pattern for option handling
61-62: Verify samtools regions-file option compatibility.
Let's verify that --regions-file is the correct option name across different samtools versions.
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🧹 Outside diff range and nitpick comments (1)
snakemake_wrapper_utils/samtools.py (1)
32-32: Fix typo in error messageThe word "infered" should be "inferred".
- "You have specified number of threads (`-@/--threads`) in `params.extra`; this is automatically infered from `threads`." + "You have specified number of threads (`-@/--threads`) in `params.extra`; this is automatically inferred from `threads`."
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snakemake_wrapper_utils/samtools.py (1)
Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.
🔇 Additional comments (3)
snakemake_wrapper_utils/samtools.py (3)
15-15: LGTM: New parameter follows established patterns
The parse_regions parameter is well-named and follows the existing pattern of boolean flags for controlling option parsing.
52-62: LGTM: Clean implementation of regions file parsing
The implementation follows the established pattern and handles both variants of the regions file option consistently.
56-59: Verify samtools CLI compatibility
Let's confirm that both --region-file and --regions-file options are valid in samtools and that --regions-file is the preferred option.
Parse regions file for samtools
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