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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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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.

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output all possible subgraphs #18

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