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Implement Chop #188

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Implement Chop #188

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Commits on Jun 10, 2024

  1. typo

    @susan-garry
    susan-garry committed Jun 10, 2024
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Commits on Jun 14, 2024

  1. initial chop implementation

    @susan-garry
    susan-garry committed Jun 14, 2024
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Commits on Jun 17, 2024

  1. test chop, fix off-by-one error

    @susan-garry
    susan-garry committed Jun 17, 2024
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  2. test fgfa depth

    @susan-garry
    susan-garry committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. typo

    @susan-garry
    susan-garry committed Jun 18, 2024
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  2. add benchmarking for chop, allow shell commands in config.toml (so we… 

    … can pipeline)
    @susan-garry
    susan-garry committed Jun 18, 2024
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Commits on Jul 6, 2024

  1. chop now computes new links, but is buggy (as is odgi), testing frame… 

    …work
    @susan-garry
    susan-garry committed Jul 6, 2024
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Commits on Jul 8, 2024

  1. re-implement chop treating links as bidirectional, tests pass

    @susan-garry
    susan-garry committed Jul 8, 2024
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  2. clippy

    @susan-garry
    susan-garry committed Jul 8, 2024
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  3. turnt error messages are verbose

    @susan-garry
    susan-garry committed Jul 8, 2024
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  4. flatgfa now requires odgi and slow_odgi

    @susan-garry
    susan-garry committed Jul 8, 2024
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  5. make fetch-og generates odgi files, which test-flatgfa depends on

    @susan-garry
    susan-garry committed Jul 8, 2024
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  6. Get changes to workflow file

    @susan-garry
    susan-garry committed Jul 8, 2024
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  7. flatgfa tests display turnt diffs

    @susan-garry
    susan-garry committed Jul 8, 2024
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  8. tests that rely on odgi use odgi files, avoids unnecessary conversions

    @susan-garry
    susan-garry committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. turnt prints stuff

    @susan-garry
    susan-garry committed Jul 9, 2024
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  2. use latest version of odgi

    @susan-garry
    susan-garry committed Jul 9, 2024
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  3. actually run tests, don't just print turnt commands

    @susan-garry
    susan-garry committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. simplifications, code comments, and better benchmarking

    @susan-garry
    susan-garry committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. represent the ranges of newly chopped segments as spans; abstracting … 

    …away spans and ids would be nice, but if we're using ids, we might as well use spans
    @susan-garry
    susan-garry committed Jul 11, 2024
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  2. oops

    @susan-garry
    susan-garry committed Jul 11, 2024
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