add bigwig support?

[andrewejaffe]

should be fairly straightforward, instead of:

align = Rsamtools::readGAlignments(bam)
coverage(align)

you can just do:
rtracklayer::import.bw(bigwig, asRle=TRUE)

which is already a coverage RleList. Note there is also support for going chromosome by chromosome with the which input like Rsamtools.

it seems faster than reading in the bams as well

[lcolladotor]

Note BigWig is not supported on Windows. Warnings will be shown if a Windows users tries to interact with BigWig files.