Using Alt+Ref instead of true depth

[arichards2564]

https://github.com/mskcc/facets-suite/blob/41a01fe9afb947f38af2802cf62189e0a1061cc5/R/ccf-annotate-maf.R#L58

Here, we overwrite the true read depth with alt+ref. Normally, this doesn't change much but I've seen positions where there are 3 alleles present at a given position and the mutation being called is not the major allele and neither is the reference allele. This changes the calculation quite a bit.