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Add bigbed to bed converter and tests #19787

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Merged
merged 3 commits into from
Mar 21, 2025

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d-callan
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adding a bigbed to bed datatype converter. see galaxyproject/brc-analytics#371

How to test the changes?

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  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

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  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@d-callan
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does this need anything else from me? im not sure i understand the failures tbh..

@mvdbeek mvdbeek force-pushed the bigbed-to-bed-converter branch from ea821b8 to f538d8f Compare March 17, 2025 13:55
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mvdbeek commented Mar 17, 2025

Can you take a look at the artefacts in https://github.com/galaxyproject/galaxy/actions/runs/13901245452?pr=19787 ? The first 3 tests are failing. <output name="bed_output" value="output.bed" ftype="bed"/> means that we're expecting an exact match between what the converter generates and the output file that you've included in the PR. You can use any of the assert_contents statements and remove the explicit comparison with output.bed. has_n_lines (https://docs.galaxyproject.org/en/latest/dev/schema.html#has-n-lines) would be enough I think.

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mvdbeek commented Mar 21, 2025

Thanks @d-callan!

@mvdbeek mvdbeek merged commit 1677657 into galaxyproject:dev Mar 21, 2025
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@galaxyproject galaxyproject deleted a comment from github-actions bot Mar 21, 2025
@ahmedhamidawan ahmedhamidawan changed the title bigbed to bed converter and tests Add bigbed to bed converter and tests May 13, 2025
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3 participants