First time tagging heterozygous pair on variant search messes up tags on variants

[NLSVTN]

When we tag a heterozygous pair on variant search page the first time (create_saved_variant_handler method called), the following piece of code does not correctly fill up 'variantGuids' parameter in each tag which causes a bug when the returned 'variantTagTypes' contains only tags with a single item in 'variantGuids' instead of two for pairs:

https://github.com/macarthur-lab/seqr/blob/master/seqr/views/utils/orm_to_json_utils.py#L416

It then shows tags incorrectly. Reloading the page fixes the issue.

Here is how the bug looks like on a single pair. Before tagging:

After tagging:

It can also be an issue of creating/deleting tags when same variants are in different pairs. Not fully sure.

To reproduce the bug you can do the following:

1. Do the search with such parameters selected:

2. Find first two ZNF717 gene pairs and assign pair and individual tags to the first pair

3. Assign pair tag to the second ZNF717 gene pair and check how the first started to look like

[hanars]

Can you confirm that you are using the latest version of the code when you are experiencing this issue? Can you also send a screenshot of the footer of the page, which includes the seqr version that can help me debug

[NLSVTN]

Ok, will do.

[NLSVTN]

Unfortunately, its not possible because we need to modify postgres due to the new fields added. So, after I pulled the code I am getting an error 'column seqr_individual.sv_flags does not exist LINE 1: ...latform_filters", "seqr_individual"."population", "seqr_indi... ^'. But if there were no changes in the handler that creates the variants and update variant functions, create tags function, the bug should be there, I think. What happens it seems is when we do tagging in variant search, tags are created wrongly, so VariantTag model then contains wrong elements which then show up.

I reversed back to the version that has the bug and it is the following (from the footer): seqr v1.0-3d8d6a9d

[NLSVTN]

No, its not wrong DB modification, sorry, DB seems fine, but the bug still happens.

[NLSVTN]

When the iteration happens here:

https://github.com/macarthur-lab/seqr/blob/master/seqr/views/utils/orm_to_json_utils.py#L421

The tags for pairs of the other pair (not currently being tagged) are returned with only one item in 'variantGuids' list.

[NLSVTN]

It happens because the saved variants in the pair being tagged are not all saved variants there we need to consider to fill up 'variantGuids':

Pair being tagged has variants 1 and 2 Another pair has variants 1 and 3

If we assign a tag to the first pair, we are leaving out the 3rd from the picture, so the 'variantGuids' of the tags assigned to the second pair will have only one item. We either need to exclude these tags from iteration or fill them up correctly.

[NLSVTN]

So, I think this line needs to be modified:

https://github.com/macarthur-lab/seqr/blob/master/seqr/views/utils/orm_to_json_utils.py#L410

I am looking into it, will let you know if I manage to fix it

[NLSVTN]

Ok, I fixed it but not in a beautiful way:

In create_saved_variant_handler I pass 'paired' parameter to the 'get_json_for_saved_variants_with_tags' function:

paired = isinstance(variant_json['variant'], list) 
response_json = get_json_for_saved_variants_with_tags(saved_variants, paired=paired, add_details=True)

Then, in get_json_for_saved_variants_with_tags:

 tag_models = VariantTag.objects.filter(id__in=variant_tag_id_map.keys())                                               

    if paired:                                                                                                             
        variant_ids = saved_variant_id_map.keys()                                                                          
        for idx, variant_id in enumerate(variant_ids):                                                                     
            tag_models = tag_models.filter(saved_variants=variant_ids[idx]) 

So, when we do tagging by pair we limit our tags only to the ones that have both variants in saved_variants list. Maybe you could fix it in a more elegant way.