Manual create variant - polling hangs forever if variant is normalized

[davmlaw]

Search for "NC_000009.12:g.1005_43466del" and then create it

Bcftools normalizes it, and changes ref

Then in ManualVariantsPostInsertTask

• variant_pk_lookup adds the variant, but the hash is different as it was normalized
• We loop over variant_pk_by_hash - looks like we expect there to be variant_pk of None, but this will never happen, as in that case, the variant would have turned up in unknown_variant_coordinates
• We then miss the variant, don't make any CreatedManualVariant objects, and the polling hangs forever

I think a simple fix would be to move the variant_pk is None work into processing unknown_variant_coordinates

[davmlaw]

If you create "NC_000009.12:g.5_43366del" it also dies as it's removed by clean and filter

• We should probably parse the reject pile here? Even if we fix below
• vcf_clean_and_filter - ref_standard_bases_pattern needs to include an N to allow these to go through as well

[davmlaw]

testing vg test - passed

NC_000009.12:g.1005_43466del - works, comes up with normalization message NC_000009.12:g.5_43366del - works, comes up with normalization message

[EmmaTudini]

Re-opened as admins can create variants in Shariant - low priority for testing We do not manually create variants in Shariant so should be safe. That said, admins still have the ability to do so, so you can always search for the “g.” that Dave lists in the issue and create it