Use of t_depth vs. t_alt_count + t_ref_count

[andurill]

Hi,

There is a minor error here: https://github.com/mskcc/facets-suite/blob/master/R/ccf-annotate-maf.R#L29. The check is for the presence of t_alt_count and t_ref_count columns, but the error message is "Columns t_alt_count and t_depth required."

Also, in the same module, I think it will be useful to add an optional argument to enable using t_depth values present in the maf file directly for calculating t_var_freq, instead of calculating t_depth as t_alt_count + t_ref_count. This is because: 1.) In multi-allelic sites, calculating t_depth as t_alt_count + t_ref_count might be incorrect. 2.) Although rare, in some input maf files, only the t_depth and t_alt_count columns are populated. This causes NA to be coerced for all columns related to ccf.

I made the update above for my usage. If this of any interest to you, I'm happy to do a PR.