Error with annotation

[jharenza]

          @kgaonkar6 , @jharenza  

Y have error for annotated fusion call from arriba and Star-fusion. Y use annoFuse:

Warning messages: 1: Expected 2 pieces. Missing pieces filled with NA

Originally posted by @serignebasse in https://github.com/d3b-center/annoFuse/issues/85#issuecomment-1906887707

[serignebasse]

thanks you @jharenza, y use annotate_fusion_calls: Function to annotate fusion calls. Y tried with Example star fusion and arriba fusion input files found in annoFuseData but y get same error

[federicomarini]

I am not entirely sure the message you obtained is indicative of an error per se, but it just seems to be a warning.

Could you provide us with some form of an example we can try to reproduce on our ends? Either a self contained snippet using the example data (if you have the message on that) or the code&data you are using when the message is triggered.

[serignebasse]

@federicomarini it is the same error when I use the example data in annoFuse. Y used the code and example data in the documentation without changing anything. But Y get this error. Y don't have results.

[serignebasse]

the error is in the Standardised function Y thinks, like: standardizedArriba<-fusion_standardization(fusion_calls = fusionfileArriba, caller = "ARRIBA", tumorID ='tumorID')

[federicomarini]

I just tested running the whole set of examples on the package as it is now in the master codebase, and I was not able to reproduce the error you mention. Can you please try to update your local installation to the latest version?

Again, if all you see is

Warning messages:
1: Expected 2 pieces. Missing pieces filled with NA

that is just a warning message. Some fields which were left empty has likely become an NA.

@jharenza do you have the same experience with this?