R/read_tab_generic.R

In genio: Genetics Input/Output Functions

# this abstracts general tab reading regardless of specifics of some of the various formats supported
read_tab_generic <- function(
                             file,
                             ext,
                             tib_names,
                             col_types,
                             verbose = TRUE, 
                             comment = '#'
                             ) {
    # check that mandatory arguments aren't missing
    if (missing(file))
        stop('Input file path (file) is required!')
    if (missing(ext))
        stop('Input extension (ext) is required!')
    if (missing(tib_names))
        stop('Table column names (tib_names) is required!')
    if (missing(col_types))
        stop('Table column types (col_types) is required!')
    
    # add .ext and/or .gz if missing and needed
    file <- add_ext_read(file, ext)
    
    # announce what we ended up loading, nice to know
    if (verbose)
        message('Reading: ', file)
    
    # read input
    ind <- readr::read_table(
                      file,
                      col_names = tib_names,
                      col_types = col_types,
                      comment = comment
                  )
}