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[WIP] Improve off-reference coordinate and rGFA support #3891

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wants to merge 21 commits into from
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[WIP] Improve off-reference coordinate and rGFA support #3891

wants to merge 21 commits into from

Commits on May 4, 2023

  1. init rgfa commit

    @glennhickey
    glennhickey committed May 4, 2023
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  2. clean up recursion a bit

    @glennhickey
    glennhickey committed May 4, 2023
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  3. implement greedy rgfa optimizer

    @glennhickey
    glennhickey committed May 4, 2023
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  4. rgfa forwardization

    @glennhickey
    glennhickey committed May 4, 2023
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  5. start rgfa tests

    @glennhickey
    glennhickey committed May 4, 2023
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  6. ../src/gfa.cpp 

    rgfa strand swtiching test
    @glennhickey
    glennhickey committed May 4, 2023
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  7. fix strand bug

    @glennhickey
    glennhickey committed May 4, 2023
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  8. use better serilization call in paths (that supports gfa in/out)

    @glennhickey
    glennhickey committed May 4, 2023
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  9. add missing test file

    @glennhickey
    glennhickey committed May 4, 2023
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  10. some ui tweaks for rgfa

    @glennhickey
    glennhickey committed May 4, 2023
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  11. fix assertion fails that happen in full hprc graph

    @glennhickey
    glennhickey committed May 4, 2023
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  12. pivot to store rgfa info in locus

    @glennhickey
    glennhickey committed May 4, 2023
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Commits on May 10, 2023

  1. parameterize rgfa sample name

    @glennhickey
    glennhickey committed May 10, 2023
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Commits on May 11, 2023

  1. adapt rgfa tests to latest conventions

    @glennhickey
    glennhickey committed May 11, 2023
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Commits on May 17, 2023

  1. leave subpath *in* rgfa names in surject (for now)

    @glennhickey
    glennhickey committed May 17, 2023
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Commits on May 20, 2023

  1. write all context metadata inside rgfa pathname

    @glennhickey
    glennhickey committed May 20, 2023
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Commits on May 25, 2023

  1. fix some rgfa naming details

    @glennhickey
    glennhickey committed May 25, 2023
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Commits on May 26, 2023

  1. yet another parent path layout

    @glennhickey
    glennhickey committed May 26, 2023
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Commits on May 29, 2023

  1. fix typo

    @glennhickey
    glennhickey committed May 29, 2023
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  2. handle duplications when annotating parent paths

    @glennhickey
    glennhickey committed May 29, 2023
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  3. more cycle edge cases

    @glennhickey
    glennhickey committed May 29, 2023
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