Add contig_lengths dataset attribute if found in the VCF file
#946
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benjeffery
approved these changes
Nov 2, 2022
| @@ -525,6 +525,10 @@ def vcf_to_zarr_sequential( | |||
| ds.attrs["filters"] = filters | |||
| ds.attrs["vcf_zarr_version"] = "0.1" | |||
| ds.attrs["vcf_header"] = vcf.raw_header | |||
| try: | |||
| ds.attrs["contig_lengths"] = vcf.seqlens | |||
| except AttributeError: | |||
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Checking the cyvcf2 source I see that this raises if the lengths are absent in the header, so seem ok to then omit them in our output.
The mandatory ones are listed on https://github.com/pystatgen/vcf-zarr-spec/blob/main/vcf_zarr_spec.md#vcf-zarr-group-attributes. Perhaps we should add this one as an optional attribute there? |
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Part of #464, and needed for tskit-dev/tsinfer#748