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noodles-htsget based refactor #89

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brainstorm opened this issue Jun 3, 2022 · 3 comments
Open

noodles-htsget based refactor #89

brainstorm opened this issue Jun 3, 2022 · 3 comments
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enhancement New feature or request

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@brainstorm
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brainstorm commented Jun 3, 2022

Revisit noodles newest changes on noodles-htsget crate and refactor our htsget-search accordingly: https://github.com/zaeleus/noodles/commits/master/noodles-htsget

@brainstorm brainstorm self-assigned this Jun 6, 2022
@brainstorm brainstorm changed the title [chore] Noodles refactor and improve CI caching noodles-htsget based refactor Jun 14, 2022
@brainstorm brainstorm removed their assignment Jun 29, 2022
@brainstorm brainstorm added the enhancement New feature or request label Jun 30, 2022
@mmalenic
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Closed via #122, and small changes in various other pull requests.

@brainstorm
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brainstorm commented Dec 15, 2022

@mmalenic Are we really reusing functionality from noodles-htsget? I cannot see it even being imported on https://github.com/umccr/htsget-rs/blob/main/htsget-search/Cargo.toml :/

IIRC, when looking at the noodles-htsget crate, we concluded that we could nuke a ton of our own htsget-search crate, and it doesn't look like that right now?

Let me know if I'm wrong, if I'm not, reopen please ;)

@mmalenic
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My bad! For some reason I had completely forgotten about that side of noodles. You're right, some of the structs look like they could be used from noodles-htsget (although it seems like parts of it are private), although most of the 'searching' logic would still need to be ours I think.

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