Using Alt+Ref instead of true depth

[arichards2564]

facets-suite/R/ccf-annotate-maf.R

Line 58 in 41a01fe

maf[, t_depth := t_alt_count + t_ref_count]

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.