Enable the usage of custom genome and exome in whichSignatures

[Yunuuuu]

Now, whichSignatures only can use default hg19 to calculate counts fraction, this commit just add two arguments - genome.ref and exome.range.

genome.ref accept a BSgenome object to define the genome used to calculate tri.counts.wgs, so we can use a lot of reference genome (as provided by Bioconductor or read fasta file and construct one by ourself).

exome.range accept a GenomicRange object to define the exon ranges to calculate tri.counts.wes

[Yunuuuu]

This commit also re-construct data structure to fix #74