docs: review fixes + relocate get_regions_file.py#97
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Pull request overview
Documentation polish and a file relocation: moves the BGSignature regions-file helper out of the MANE preprocessing toolkit into the mutation-profile tools directory, and updates the docs accordingly. Also surfaces a couple of CLI/pipeline flags in the docs (per PR description).
Changes:
- Relocate
tools/preprocessing/get_regions_file.py→tools/mut_profile/get_regions_file.py. - Update
docs/run_input_output.mdpaths to reflect the new location.
Reviewed changes
Copilot reviewed 1 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| tools/mut_profile/get_regions_file.py | New location of the BGSignature regions-file helper (content unchanged). |
| docs/run_input_output.md | Updates the script path references to the new location. |
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tools/preprocessing/get_regions_file.py→tools/mut_profile/get_regions_file.py. The MANE preprocessing toolkit (with its ownpyproject.toml) was the wrong home for a BGSignature regions-file helper.docs/run_input_output.md.