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Infer count matrix strands from RSeQC output#14

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iamh2o wants to merge 22 commits intocodex/refactor-script-directives-to-shellfrom
codex/update-count_matrix-rule-for-params.strans
Open

Infer count matrix strands from RSeQC output#14
iamh2o wants to merge 22 commits intocodex/refactor-script-directives-to-shellfrom
codex/update-count_matrix-rule-for-params.strans

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@iamh2o iamh2o commented Sep 19, 2025

Summary

  • parse RSeQC infer experiment outputs to determine per-sample strand settings for the count matrix rule
  • fall back to configured strandedness values when inference files are missing or inconclusive

Testing

  • not run (not requested)

https://chatgpt.com/codex/tasks/task_e_68ccb6274c448331bae65cf600221298

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