#' Reads data from a single DSSAT output file
#'
#' @export
#'
#' @inheritParams read_dssat
#'
#' @inheritParams read_tier_data
#'
#' @return a tibble containing the data from the raw DSSAT output
#'
#' @importFrom readr cols col_character
#' @importFrom stringr str_subset str_which
#' @importFrom dplyr "%>%"
#' @importFrom purrr map reduce
#'
#' @examples
#'
#' # Extract file path for sample output file path
#' sample_output <- system.file('extdata','SAMPLE.OUT',package='DSSAT')
#'
#' out <- read_output(sample_output)
#'

read_output <- function(file_name, col_types = NULL, col_names = NULL,
                        left_justified = NULL, read_only = NULL,
                        store_v_fmt = FALSE){

  col_types <- cols(` TNAME\\.*`=col_character(),
                    ` TNAM\\.+`=col_character(),
                    ` EXNAME\\.*`=col_character(),
                    `EXCODE  `=col_character(),
                    ` FNAM\\.*(?= |$)`=col_character(),
                    ` WSTA\\.*`=col_character(),
                    ` SOIL_ID\\.*`=col_character(),
                    ` MODEL\\.*`=col_character()) %>%
    {.$cols <- c(.$cols,col_types$cols);.}

  left_justified <- left_justified %>%
    c(.,' TNAME\\.*',' TNAM\\.+',' EXNAME\\.*',' FNAM\\.*(?= |$)',' WSTA\\.*',
      ' SOIL_ID\\.*',' MODEL\\.*','EXCODE  ')

  col_names <- col_names %>%
    c(.,
      ' +S(?= |$)',' +O(?= |$)',' +C(?= |$)',' +CR(?= |$)',' TNAM(?= |$)','  TRNO')

  # Read in raw data from file
  raw_lines <- readLines(file_name) %>%
    str_subset('^(?!\032) *([^ ]+)') # exclude lines that are all spaces or lines with EOF in initial position

  # Find beginning of each section
  begin <- raw_lines %>%
    str_which('^\\*DSSAT')

  if(length(begin)==0) begin <- 1

  # Calculate end of each section based on beginning of next section
  end <- c(begin[-1]-1,length(raw_lines))

  # Read each section of output file
  output <- map(1:length(begin),
                   ~read_tier(raw_lines[begin[.]:end[.]],
                              col_types = col_types,
                              col_names = col_names,
                              left_justified = left_justified,
                              store_v_fmt = store_v_fmt,
                              read_only = read_only)) %>%
    reduce(combine_tiers) %>%
    as_DSSAT_tbl()

  return(output)
}