[Feature request] option to filter alignments based on annotation type

[elhossary]

Option to filter alignments based on annotation type, for example, RNA-Seq can contain ribosomal RNA reads. if no proper rRNA depletion was done to the sample, they can be the majority of the reads. Thus, when aligned, and coverage computed based on their presence, the can affect the normalization. So, In some use cases they need to be removed from the alignment before coverage generation.
This can be easily aceived by "bedtools intersect" which accepts BAM files as will as GFFs and can be used to filter them