Implemented Bioconductor suggestions

Changed version number to 0.99.2.

Implemented the following changes (this text is also in the NEWS document):

CHANGES IN VERSION 0.99.2
-------------------------

NEW FEATURES

    o made aldex.clr into a class

    o allowed input of SummarizedExperiment object instead of a reads data frame

    o prioritized use of the BiocParallel package for multicore processing. If BiocParallel is not installed then the parallel package used, if neither packages are installed, then serial processing is used