Variant zmenu payload

[azangru]

Update zmenu payload for variants to enable navigation to other variants within genome browser

• add region name
• add start coordinate (adding 1 to translate from bed coordinate system to ensembl coordinate system)
• add end coordinate

Example link for review deployment: http://variant-link-zmenu.review.ensembl.org/genome-browser/grch38?focus=variant:1:911996:rs777886556

[veidenberg]

To add context for commits, this PR is also testing new variation datafiles.

[veidenberg]

The +1 change in the zmenu start coordinate doesn't show up in GB? The example rs777886556 has 911996 start coordinate in BED file, so should be shown as 911997 in GB (but I see 911996 in review app).

[azangru]

The +1 change in the zmenu start coordinate doesn't show up in GB?

@veidenberg that's because 1 is subtracted from the start coordinate before passing the variant data to the zmenu function here:

https://github.com/Ensembl/ensembl-dauphin-style-compiler/blob/master/backend-server/egs-data/egs/v16/variant/variant-dbsnp-detail.eard#L68

Here's what I can see in the genome browser client's logs put inside the zmenu function: the first line in the log below is the variant name, the second is the start coordinate as it is passed to the zmenu function, and the third is the corrected start coordinate after 1 is added to it.

So the zmenu function is working correctly; it is the -1 in the data retrieval function that leads to an unexpected result.