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Autoindex should parse tabix-indexed monolithic VCFs in parallel #4277

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jeizenga opened this issue Apr 25, 2024 · 0 comments
Open

Autoindex should parse tabix-indexed monolithic VCFs in parallel #4277

jeizenga opened this issue Apr 25, 2024 · 0 comments

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@jeizenga
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We've had a few users complain about autoindex's excessively slow chunking process for VCFs when they are provided as a single file for all chromosomes (e.g. #4274). This results from a single-threaded linear scan over the VCF to parcel it out to chunks that subsequently run in parallel. If the VCF is tabix-indexed, it should be possible to chunk the VCF in parallel across chromosomes, which would alleviate this issue.
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@jeizenga