Things to do for easier use

[ ] addReadStats is too slow
[ ] filterReads is too slow
[x] filterReads could return the filter statistics (without subsetting the se)
[x] subsetReads fails if non-existing read ids are provided
[x] plotRegion fails if empty list is given to a track argument
[x] plotRegion does not allow to change the size of lollipops (autoscale, allow user to set)
[ ] plotRegion should accept additional tracks (gene annotation, CpG island annotation, bigwig file, bed file, ...)
[ ] plotRegion improve read clustering/ordering (maybe only based on user-provided region)
[ ] plotRegion improve "Smooth" plottype
[ ] export an se (selected summary assay) as bedGraph or similar (for display in external genome browser)
[ ] add shaded background representing error bars to the smooth averages in plotRegion
[ ] allow plotRegion to use either relative or absolute position on the x-axis
[ ] add argument to add scale bar to plotRegion
[ ] plotRegion (Heatmap) doesn't deal well with situations where some position or read is all NA (at least this is what we think is the reason)
[x] linewidth in lollipops need to be adjustable too (not just the size)
[ ] describe read sampling in vignette (with random number seed)
[ ] section about parallelization in vignette (many functions use parallelization, can use register() to set default backend, ...)
[ ] messages raised in read_modbam_cpp are not always displayed in the console
[ ] lift out helper functions to calculate read statistics, vectorize when possible

fmicompbio / footprintR