Refactor input files#171
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… into its own class AND the frag_generator function into its own module.
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Note: this should merge after #170 . |
Restore handle compatibility, repair flake8 failures, and drop unsupported Python 3.9 metadata
Restore tabix genome-wide counting semantics and raise support metadata to Python 3.11
Use a Python-version-specific SciPy pin and re-enable 3.10 in CI
Filter parsed CLI args against target function signatures and add a coverage smoke test.
Compare DELFI outputs from the existing 2-bit fixture and a matching FASTA fixture to cover the new reference backend.
Kudostoy0u
previously approved these changes
Apr 30, 2026
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Refactors look good in current state
edawson
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Kudostoy0u’s stale review
The merge-base changed after approval.
Kudostoy0u
approved these changes
May 4, 2026
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Refactors look good in current state
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This PR refactors input files (BAM/CRAM/SAM/Frag(.gz)) behind a common interface, with all validation occurring in that class rather than the
frag_generatorfunction. This allowed streamlining the logic infrag_generatorto be less branchy. Asfrag_generatorseems to be the single most important function in this repo, I've refactored it into its own module. This required breaking dependency cycles, soutils/now includes a number of new modules.Unfortunately this touches nearly every module in the package, but most of the edits are minor. Again, happy to answer questions and contribute to testing if needed.
Tests: