search

Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
170 stars 44 forks source link

JSONDecodeError: Expecting property name enclosed in double quotes #65

Closed matteofloris closed 2 years ago

matteofloris commented 2 years ago

Hi, I just annotated my vcf with Nirvana 3.18. I got this error for the first variant:

json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes

The problem is the phylopScore, which is formatted incorrectly by Nirvana. For example it reads:

"phylopScore":1,4

instead of

phylopScore":1.4

matteofloris commented 2 years ago

same problem with polyPhenScore and siftScore

anleopa commented 2 years ago

I had the same problem

rajatshuvro commented 2 years ago

I suspect this has to do with the culture settings of dotnet. Can you please let me know how decimals are printed in your language/culture?

anleopa commented 2 years ago

With "," I had to build a specific parser for these fields, but it does not happen in other fields with decimals

rajatshuvro commented 2 years ago

That explains the behavior. In Nirvana, some decimals are pre-populated while others are printed on the fly. I believe you will see this behavior with all decimals that we print on the fly.

I have created a bug ticket in our backlog to track this. https://nirvana-annotator.atlassian.net/browse/NIR-975

anleopa commented 2 years ago

Great! Thanks

rajatshuvro commented 2 years ago

Issue has been fixed in the 3.18.0 release.