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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 commented Mar 3, 2024

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.

jeromekelleher added the bug label

jeromekelleher added this to the 0.8.0 release milestone

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partition_into_regions returns empty region for all contigs in header #1200

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jeromekelleher modified the milestones: 0.8.0 release, 0.8.1

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