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teach impg to output all possible subgraphs by a given window size #15

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subwaystation opened this issue May 21, 2024 · 0 comments · May be fixed by #18
Open
5 tasks

teach impg to output all possible subgraphs by a given window size #15

subwaystation opened this issue May 21, 2024 · 0 comments · May be fixed by #18
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enhancement New feature or request

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subwaystation commented May 21, 2024 •
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  • Add parameter window_size
  • Iterate over the first PAF entry following the window_size . Emit for each window_size a PAF.
  • Collect all ranges of all collected sequences using an interval tree https://github.com/dcjones/coitrees. Maybe do some clever sorting? Not sure if required.
  • Iterate over all other PAF entries. If a window or part of a window is not yet in the interval tree, emit another PAF. Else skip it.
  • Be happy.

Maybe we can parallelize this with an atomic interval tree. But this would be the strawberry on the cake.
@subwaystation subwaystation added the enhancement New feature or request label May 21, 2024
@subwaystation subwaystation self-assigned this May 21, 2024
@subwaystation subwaystation linked a pull request May 21, 2024 that will close this issue
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output all possible subgraphs pangenome/impg
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