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partition_into_regions: CSI indexed BCFs return empty regions #1202

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jeromekelleher opened this issue Mar 3, 2024 · 0 comments
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@jeromekelleher
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Because BCF CSI indexes store information for all contigs listed in the header, we need to filter out regions that have a zero counts like here: https://github.com/jeromekelleher/bio2zarr/blob/880c3afee4465b4b94b921c815d436f3e4a78a46/bio2zarr/vcf_utils.py#L510

While returning empty contigs is reasonably harmless, it's not if there are thousands of contigs listed in the header which is common.

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