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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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Check Exomiser database compatibility #563

Open ielis opened 2 years ago

ielis commented 2 years ago

Lirical requires Exomiser variant database to run analysis with VCF file, but there are multiple variant database releases out there. We need a way to check that LIRICAL will work with a given database file to prevent violent application crashes.

gileshall commented 6 months ago

Hello,

If I use 2402_hg38 from exomiser, I get the following error: java.lang.IllegalStateException: The read format 3 is larger than the supported format 1 [1.4.200/5]

Is this expected? Is there a v1 build of 2402_hg38_variants.mv.db ?

ielis commented 6 months ago

Hi @gileshall Exomiser team changed the schema of the variant database file, and LIRICAL is not yet compatible with the new schema. This means, the database release 2402 is not yet supported, hence the error.

We plan to support the new schema, but it is not there yet. Therefore, in the short term, you can only use LIRICAL with 2309 (or older).

In the "long" term, I will update this issue when we add support for the new database schema in LIRICAL.

gileshall commented 6 months ago

Hi @ielis,

Thank you for your prompt reply. I will try with an older Exomiser variants database. However, I was curious if this was a database version issue, or if the schema also changed. The nature of the stack trace gave me the impression that the h2 library needed updating to support v3 of the database format, but I didn't drill into the actual schema. I also noticed that Lirical incorporates the Exomiser codebase for loading this database, so I was curious if this abstracted away any schema changes.

Thank you.