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@asalt asalt commented Apr 15, 2025

Purpose

when assigning confidence, a NotImplementedError is raised. I

    outfile_ext = dataset.get_default_extension()

    mokapot/mokapot/confidence.py", line 1150, in create_sorted_file_reader
    outfile_ext = dataset.get_default_extension()

    mokapot/mokapot/tabular_data/base.py", line 65, in get_default_extension
    raise NotImplementedError
NotImplementedError

I looked at importing and using CsvFileReader inside confidence.py, but became confused with the inheritance scheme of the various Dataset objects and where they were being created. Simply providing a reasonable return value solved the issue, but there may be a more preferred way to solve this.

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