1. Load data and get per-position coverage:

library(Rsamtools) 
library(bumphunter) 
pileup_df <- Rsamtools::pileup(file.path(getwd(), "datasets", "ch1", "windows.bam"))

2. Find preliminary clusters:

clusters <- bumphunter::clusterMaker(pileup_df$seqnames, pileup_df$pos, maxGap = 100) 

3. Find the bumps with a minimum cutoff:

bumphunter::regionFinder(pileup_df$count, pileup_df$seqnames, pileup_df$pos, clusters, cutoff=1)