output VCF is not spec compliant - ACMG_DISEASE_NAME can contain commas

[ameynert]

The output VCF can contain commas in the ACMG_DISEASE_NAME field of the Exomiser INFO key. Could these be replaced with semi-colons or underscores?

[Exomiser/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/VcfResultsWriter.java](

Exomiser/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/VcfResultsWriter.java

Line 241 in 421c22d

fields.add('"' + assignment.map(acmgAssignment -> acmgAssignment.disease().diseaseName().replace(" ", "_")).orElse("") + '"');

This breaks spec compliance which says "commas are permitted only as delimiters for lists of values".

Because the Exomiser INFO field is set as `Number=.' in the VCF, pysam interprets these commas as breaking between multiple instances of the field, which breaks parsing the field into its subfields.

related to #620

[julesjacobsen]

Hi @ameynert , thanks for the feedback. This is now fixed and will be released in 15.1.0