Ability to filter/discard CTSSs overlapping some genomic region(s)

[snikumbh]

Detail description:
After all the CTSSs are read from the BAM files, is there a possibility to filter out CTSSs that overlap with some genomic regions? For example, some accidental leftover rDNA regions.

While such filtering can happen downstream -- by filtering out tagClusters that overlap the said genomic regions, but keeping them could affect/bias the normalization step. Hence, completely discarding them from the CAGEr object itself would be a better approach, IMO.