After reviewing the filter names for bed and bam files I believe that there is a little bit of work to do to make these a little more clear for the user. I don't think that all the names need to be changed, but we may be able to adjust a few things here to make their functions more clear to the users.

I reviewed the filters available for bed and bam files:

Bed: Reads with gaps, Reads with no gaps, and Score
-For the Bed filters, I think it is odd that filters for bed files would be read related. It seems that the read related filters should apply to Bam files.

Bam: Average Quality Score, Filter by Strand, Mapping Quality Score, Mismatch, Multi-Mapper, Paired End Mates, Perfect Match, Reads with gaps, Reads with no gaps, Run number, Score, Single Mapper, Technical Duplicate
-For the Bam filters I believe that many of these filter names make sense. We may want to order Multi Mapper underneath Single Mapper though to illustrate that it is either multi-mapped or single mapped. I'm not sure what the difference is though between average quality score and score either. I also don't understand why filter by strand is only a filter for bam files, why not bed files too? I also do not understand what the filter Perfect Match does.