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Add x-mapper support #272

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Add x-mapper support #272

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@wwood wwood commented Sep 2, 2025

Summary

  • add X-Mapper as a mapping option with parameter passthrough
  • skip pre-indexing and command generation for X-Mapper
  • test x-mapper command construction
  • add optional integration tests that download X-Mapper, verify it outputs SAM, and ensure coverm make -p x-mapper generates a valid BAM

Testing

  • cargo test
  • cargo test x_mapper -- --ignored

https://chatgpt.com/codex/tasks/task_e_68b66f1c253c832abf4867781a902d18

@wwood wwood mentioned this pull request Sep 2, 2025
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@wwood