Correct allelic copy number results

[Gavin Ha]

The introduction of the functions correctIntegerCN and logRbasedCN to corrects total copy number. This is done by taking the original log ratio input value for a segment and/or bin and computing an absolute copy number value by correcting for the estimated purity and ploidy. This mainly addresses the problem of a finite copy number state space which is usually capped at 8 copies. Using this correction, events with more copies than 8 will be adjusted to their likely copies.

Now, I will also correct allelic copy number using a similar idea. I will modify the correctIntegerCNand add a new internal function allelicRatioBasedCN that recomputes the allelic copies following this adjustment.

This will help to address a previous issue #57