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Avoid full length sequence fetch on SNP coverage calculation #4708

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merged 1 commit into from
Dec 10, 2024

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This PR #4647 which addressed primarily rendering modifications made a large number of refactors to make rendering modifications and methylation improved

In the process it introduced a change that fetched the entire sequence. However, there are some cases where

a) jbrowse will decide to render when you are zoomed out super far (for e.g. targetted sequencing)
b) then it will fetch an entire chromosomes worth of data

there is an additional thing where maybe there is something else combining the requests because the indexedfastaadapter is designed to break up requests into smaller chunks, but a user was observing that it was making a single(?) huge HTTP Range request and this was rejected by google cloud servers

@cmdcolin cmdcolin changed the title Revert full length sequence fetch on SNP coverage calculation Avoid full length sequence fetch on SNP coverage calculation Dec 10, 2024
@cmdcolin cmdcolin merged commit 7401074 into main Dec 10, 2024
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@cmdcolin cmdcolin deleted the revert_full_length_sequence_fetch_snpcov branch December 10, 2024 19:37
@cmdcolin cmdcolin added the bug Something isn't working label Dec 10, 2024
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