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Added optional SC tag to GFA2, similar to GFA1.2 + readme update #116

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Added optional SC tag to GFA2, similar to GFA1.2 + readme update #116

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Commits on Apr 7, 2022

  1. added gfastats to the list of tools supporting gfa2 and proposed spec… 

    …ification for cuts in segments

As discussed today with @lh3, I am proposing to allow optional specification of subsequences directly in a path component, e.g. e.g. ptg000124l.1(397101:505533)+

We have devised a new tool (gfastats) that can take an agp file, for example from a scaffolding tool, and overlay the information on the original graph. When cuts are made within contigs, the segment is unmutable but we represent this event with coordinates associated to the component in the path, allowing to easily identify where cuts have occurred in the original segments
    @gf777
    gf777 committed Apr 7, 2022
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Commits on May 23, 2022

  1. Update GFA1.md

    @gf777
    gf777 committed May 23, 2022
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Commits on May 31, 2022

  1. Update GFA1.md

    @gf777
    gf777 committed May 31, 2022
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  2. reverting commit to split pull request

    @gf777
    gf777 committed May 31, 2022
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Commits on Jun 2, 2022

  1. v1.2 features revision 

    Some discussion points marked by TODO
    @snurk
    snurk committed Jun 2, 2022
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Commits on Jun 3, 2022

  1. Addressing comments 

    Addressing comments by @asl, no more TODOs
    @snurk
    snurk committed Jun 3, 2022
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  2. Addressing comments 

    Addressing comments by @lh3
    @snurk
    snurk committed Jun 3, 2022
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Commits on Jun 7, 2022

  1. Update GFA1.md 

    Misprint fix
    @snurk
    snurk committed Jun 7, 2022
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Commits on Jun 16, 2022

  1. Update GFA1.md 

    Fix SC tag
    @snurk
    snurk committed Jun 16, 2022
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Commits on Jun 17, 2022

  1. added shortcut spec also to GFA2 

    Based on the specifications of GFA1.2, a tag is added to indicate specific shortcut connections of assembly scaffolds (as opposed to missed overlaps or missing sequence during graph construction)
    @gf777
    gf777 committed Jun 17, 2022
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  2. updated readme files

    @gf777
    gf777 committed Jun 17, 2022
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  3. Merge branch 'GFA-spec:master' into master

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    gf777 committed Jun 17, 2022
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