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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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TSV output when using yaml files #577

Closed evatosco closed 1 year ago

evatosco commented 2 years ago

Hello again!

I have created a previous issue, I swear I am not trying to be annoying. The tool works well! I have been using yaml files (VCF+HPO) as input, and I have a little problem, not really that big of a deal: the docu says that if I add --tsv it will generate also a tsv output, which would be a lot easier for me to analyze. When I try to do this, it only generates HTML files: java -Xms2g -Xmx6g -jar ./*.jar yaml -y /user/folders/lirical_YMLs/LIRICAL_example.yml --tsv

I cannot find the tsv files. I have tried using --tsv=true , changing the order of the code, but the HTML file is the only output file I see. Maybe there is something I am missing here. If anyone can help me with this, I would really appreciate it. Is the --tsv option only available for Phenopackets input?

Thank you so much in advance!

ielis commented 1 year ago

Hello @evatosco , similar to #576 , this bug was resolved in the v2.0.0-RC1 version, where we extensively revisited the CLI to ensure creation of all requested result output formats. The details will be explained in the documentation, that we'll write in the next few weeks. However, I can write detailed instructions for you if you'd like to use the bleeding edge v2.0.0-RC1 release.

Thank you and all the best, Daniel

iimpulse commented 1 year ago

607