Open jeromekelleher opened 4 months ago
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.
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.