Intergenic classifications - missing c.HGVS treated as error

[davmlaw]

Create an intergenic classification, for instance:

NC_000009.12:g.99087902A>C

This is intergenic, so will have no transcript thus no c.HGVS

No c.HGVS is treated as an error, so this causes a bunch of problems:

• Resolution errors are added about missing c.HGVS
• Variant is excluded from export
• No link to allele (even though it has one) on classification page
• Link to resolution tool shouldn't appear - links as "http://localhost:8000/classification/hgvs_resolution_tool?genome_build=GRCh38&hgvs=None" which causes errors when visited

[davmlaw]

The g.HGVS is substituted for c.HGVS, which causes a spurious error about it changing (which it will as different builds have difff contig versions)

[davmlaw]

And I'm not sure why this is handled slightly differently (maybe as it tries to do HGVS as it partially overlaps a gene but can't be represented as c.HGVS as it goes off transcript), but classifying "NC_000009.12:g.99044538_99087902del", even though it has an Allele (and lifted over ok between builds):

This doesn't populate c.HGVS column on classifications grid with c.HGVS, but instead shows "not resolved, showing imported GRCh38.p14"

The resolution errors are slightly different too:

• Builds Missing 37
• Builds Missing 38

[davmlaw]

Needs to be brought up at meeting - I vote for high priority and try to get in next Shariant release