A character string indicating the path of bam file
extendReads
A logical, indicating whether reads should be extended
paired_ends
A logical, indicating whether reads are paired
fragmentLength
An integer, indicating the new size of reads when extendReads is TRUE
and paired_ends is FALSE. If NULL, read size is estimated using estimate.mean.fraglen from the chipseq package.
maxFragmentLength
An optional integer, specifying the maximal size of fragments.
Longer fragments will be disregarded when computing coverage.