Reformat af vep master

Created by: at7

Copied from #254

Requirements

NA

Description

Report allele frequencies for all alternative alleles of the input variant. This replaces the previous PR #249.

Use case

Users want to know if their input variant has know frequency data. We report the frequency from co-located variants if the input allele matches one of the alleles of the colocated variant. We then add the frequency to the output.

Benefits

Standardise how VEP reports allele frequencies across VEP script, VEP tool and REST.

Possible Drawbacks

Users need to update their parsers.

Testing

Have you added/modified unit tests to test the changes?

Yes. Updated to the newly expected json format.

If so, do the tests pass/fail?

Pass.

Have you run the entire test suite and no regression was detected?

Yes.

vep.t passes. There are errors for: t/archive.t (Wstat: 768 Tests: 10 Failed: 3) t/gene_tree.t (Wstat: 256 Tests: 41 Failed: 1) t/genomic_alignment.t (Wstat: 1536 Tests: 131 Failed: 6) t/ratelimit.t (Wstat: 768 Tests: 74 Failed: 3)

Changelog

This needs to be added instead of the current entry for [/vep/:species/*]

[/vep/:species/*] Created a frequency entry in the colocated variants entry and removed all *_maf and *_allele entries which previously reported allele frequencies. Allele frequencies are now stored in the frequency entry for a colocated variant. Allele frequencies are now reported for each alternative allele of the input variant. Allele frequencies if available are reported for the followong populations: 1000 Genomes Project: afr, amr, asn, eas, eur, sas; ESP: aa, ea; gnomAD: gnomad_afr, gnomad_amr, gnomad_asj, gnomad_eas, gnomad_fin, gnomad_nfe, gnomad_oth, gnomad_sas.