AlignedGenomeIntervals-class
                        Class 'AlignedGenomeIntervals'
addNBSignificance       assess significance of sliding-window read
                        counts
agiFromBam              Create AlignedGenomeIntervals objects from BAM
                        files.
countReadsAnnotated     Sum up aligned reads per category of genome
                        feature
fracOverlap             Retrieve intervals overlapping by fraction of
                        width
intPhred                Extract integer Phred score values from FastQ
                        data
medianByPosition        Compute median quality for each nucleotide
                        position
perWindow               Investigate aligned reads in genome intervals
                        with sliding windows
trimAdapter             Remove 3' adapter contamination
which_nearest           Methods for function 'which_nearest' and genome
                        intervals
