Hi,

I am working on a function with VCF/variants and BAM as input. The reduceByFile/reduceByRange are imported in my function, which require GRanges/GRangesList as ranges input.

However, my input requires a extented GRanges class with variants(DNAStringSet) in elementMetadata, like, CollapsedVCF.

Is it possible to extented the ranges arguments? for example, classes inherited from GRanges?

Thanks!

If you're asking about package development, then the bioc-devel mailing list is the correct place. Generally, method dispatch should work to the  'nearest' class, so if the class you are interested in contains (in S4 language) a class that is in the signature of the method you want to use, then things should 'just work'. If they do not  work, then more detail is required, in particular a reproducible example. For a package, this might require going so far as to create a small package as a github repository that captures the problem.