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genostats / Ravages

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Error regarding the path.data in RAVA.FIRST function #3

Closed LaporteFab closed 1 year ago

LaporteFab commented 1 year ago

Hi @HervePerdry,

One of my student try to use the function RAVA.FIRST() without adjCADD within the bed.matrix. Unfortunatly, the function crashed when calling the "adjustedCADD.annotation" function with this error: "the directory 'path.data' to download and use the necessary files for RAVA-FIRST analysis should be provided"

When looking at your code, i saw that the path.data given in RAVA.FIRST arguments is not passed down to the function "filter.adjustedCADD" and therefore to the function "adjustedCADD.annotation".

https://github.com/genostats/Ravages/blob/8898170d4c96bddfb592ba4e2117cbe67643a35b/R/RAVA_FIRST.r#L16 and https://github.com/genostats/Ravages/blob/8898170d4c96bddfb592ba4e2117cbe67643a35b/R/filter_adjustedCADD.r#L9

Regards, Fabien

Ozvan commented 1 year ago

Dear Fabien,

The issue has just been resolved in the GitHub version, thank you for pointing it out.

Best regards, Ozvan