fread() issue for pileup

[evanbiederstedt]

The current master branch does the following to read in the *.snp_pileup.dat.gz file

fread(sprintf('gunzip -c %s', pileup))
https://github.com/mskcc/facets-suite/blob/master/doFacets.R#L24

There's really no reason to do this. Just install R.utils as a package dependency and do fread(pileup)

I've implemented this here:
https://github.com/mskcc/facets-suite/blob/feature/just_do_fread/R/doFacets.R#L25-L31
https://github.com/mskcc/facets-suite/blob/feature/just_do_fread/NAMESPACE#L8

Reasons:
--- performance somewhat
--- remove gunzip/sprintf()
--- street cred; data.table::fread() can read in compressed files