Inter-operate with the GenomicRanges package

[adeschen]

1 - It seems like the major functions should inter-operate with the
GenomicRanges package and in particular GRanges() class. The first
two arguments of rjmcm() should be (minimally, support) GRanges
instances. The return value should be a GRanges, perhaps with
additional information in the metadata().

2 - This leads to use of S4 classes that extend GRanges, rather than ad
hoc S3 classes like rjmcmNucleosomes. The classes do not have to be
complicated, e.g.,
setClass("RJMCMNucleosomes", contains="GRanges")
with minimal additional methods, e.g., perhaps show().

[adeschen]

Done