Hi, I was trying to trying counts reads mapped onto a bed file, 

I checked the workflow of "DESeq2" , 

    gtffile <- ("mm9genes.gtf") 
    library("GenomicFeatures")
    (txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character()))
    (ebg <- exonsBy(txdb, by="gene"))
    library("GenomicAlignments")
    library("BiocParallel")
    register(MulticoreParam())
    se <- summarizeOverlaps(features=ebg, reads=bamfiles,
                             mode="Union",
                            singleEnd=TRUE,
                           ignore.strand=TRUE,
                          fragments=FALSE )  

I am not sure I understood the code completely, but my understanding is that they extract the exons locations grouped by genes (by using GenomicFeatures packages), and do the counting. 

but what if I want to count the reads overlap with genomic features described in a bed file or gtf converted from the bed file? the counterpart of "ebg" in the example.

I think you misunderstand the code. You are defining genomic regions of interest (exons), based on the GFF file, and then you are counting up all the reads from your bamfiles that overlap these regions of interest, using summarizeOverlaps.