Train-data-creator doesn't take multiple SYMBOL (ID's) into account

[SietsmaRJ]

Describe the bug

A "GENEINFO" entry can contain multiple SYMBOL (ID's):

##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">

Example:

1 1474871 1295591 G C . . ALLELEID=1285386;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.1474871G>C;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=TMEM240:339453|LOC121967044:121967044;MC=SO:0001627|intron_variant;ORIGIN=1

In this case, "LOC121967044" is discarded, which could lead to mapping problems in process-vep.

System information

• OS: Not applicable
• Version: 5.0.0.dev0
• Python version: Not applicable
• Shell: Not applicable

How to Reproduce

Steps to reproduce the behavior:

1. Run train-data-creator with a VCF containing a sample with multiple GENEINFO entries.
2. Run VEP.
3. Convert VEP output VCF to TSV.
4. Run process-vep and see that only 1 of the entries has been mapped.

Expected behavior

Currently, process-vep maps 1 to 1 from the initially supplied SYMBOL to the VEP output SYMBOL. This needs to be changed so that it maps back 1 to many (1 being the VEP output SYMBOL, many being the "ID" column SYMBOLs)

Logs

If available, the generated logging information and/or error message (can also be attached as a file if very large).

Screenshots

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Additional context

#51 (comment)