| # Repair a scientifically inconsistent HMMRATAC workflow |
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| The supplied directory contains a pinned snapshot of MACS3, including the real |
| HMMRATAC implementation used to infer accessible chromatin from ATAC-seq |
| fragments. The offline reproduction exposes an unexpected behavior: adding a |
| genomic exclusion mask can change model-input statistics and derived behavior on |
| chromosomes that are not covered by the mask. |
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| Inspect the HMMRATAC documentation in `source/` and the complete |
| fragment-to-model call graph, and repair the implementation so the exclusion mask |
| has the intended scientific meaning throughout the workflow. The repair must work |
| for ordinary paired-end fragment data and count-bearing single-cell fragment data, |
| preserve half-open interval semantics, and keep count and barcode bookkeeping |
| consistent for count-bearing fragment data. |
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|
| Duplicate retention and duplicate-related CLI naming are intentionally outside |
| the scope of this task. Preserve the existing duplicate policy and do not add, |
| remove, rename, or reinterpret duplicate flags. Repeated coordinates in the |
| fixtures are there to verify that blacklist filtering preserves the existing |
| record multiplicity and count/barcode associations. |
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| This is a capability repair, not a fixture-specific patch. Do not hard-code the |
| public chromosomes, coordinates, lengths, counts, or expected outputs. Preserve |
| the existing public workflow and keep all generated files under `outputs/`. |
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| Run the public reproduction with: |
|
|
| ```bash |
| python reproduce.py |
| ``` |
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| Treat the supplied case as one observation of the workflow defect. The repair |
| must preserve the documented scientific and record-association semantics for |
| other valid inputs supported by the same production paths. |
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|
