Switch df[,col] to df[[col]] to get column vectors

[rhagenson]

The package previously used the format df[, col] to extract a column as a vector I changed these to be df[[col]] which is compliant with more recent versions of R where df[, col] returns a data.frame with one column rather than a vector. This return type leads to expressions such as mut[, ref] %in% c('A', 'T', 'C', 'G') failing as it is not checking the values of ref, but rather the data.frame names for matching.