Handle genome FASTA inputs as forward reads #247

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wwood wants to merge 1 commit into main from codex/update-genome-fasta-pipe-mode-options

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wwood commented Aug 26, 2025

Summary

treat genome FASTA input flags like --forward
document genome FASTA usage and defaults
adjust genome tests for new behaviour
retain genome-specific default --min-orf-length
note autogenerated docs restrictions and mention genome defaults in prelude

Testing

pixi run test

https://chatgpt.com/codex/tasks/task_e_68ad18c5e1c0832a9de395be0673e9b3


          Add docs AGENTS instructions

e30f60c

wwood added the codex label

— with

ChatGPT Codex Connector

wwood force-pushed the main branch from b4bb854 to 782f1d4 Compare

November 5, 2025 03:43

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