#' Loads a fastq file
#'
#' Given a file name, it calls ShortRead::readFastq and populates the result list
#'
#' The action function for the class loadData
#'
#' @inheritParams applyOperation
#' @export
loadData <- function(all_results, config)
{
op_number <- config$current_op_number
op_args <- config$operation_list[[op_number]]
op_full_name <- paste(op_number, op_args$name, sep = '_')
op_dir <- file.path(config$output_dir, config$base_for_names, op_full_name)
dir.create(op_dir, showWarnings = FALSE, recursive = TRUE)
# input_file <- config$operation_list[[op_number]]$data_source
input_file <- op_args$data_source
if (is.null(input_file)){
stop('Input file must be specified')
}
if (!file.exists(input_file)){
stop(paste('input file does not exists: ', input_file, sep = ''))
}
max_seq <- op_args$max_seq
seq_dat <- readFastq(input_file)
total_seq <- length(seq_dat)
if (!is.null(max_seq)){
if (max_seq > 0 & length(seq_dat) > max_seq){
seq_dat <- seq_dat[1:max_seq]
}
}
per_read_metrics <- data.frame('read_exists' = rep(1, length(seq_dat)))
trim_steps <- list(step1 = list(name = 'read_exists',
threshold = 1,
breaks = c(1)))
result <- list(trim_steps = trim_steps,
metrics = list(per_read_metrics = per_read_metrics, total_seq = total_seq))
class(result) <- 'loadData'
if (op_args$cache){
result$seq_dat <- seq_dat
}
result$input_dat <- seq_dat
result$config <- list(op_number = op_number,
op_args = op_args,
op_full_name = op_full_name,
op_dir = op_dir)
return(result)
}
computeMetrics.loadData <- function(result, config, seq_dat)
{
return(result)
}
saveToDisk.loadData <- function(result, config, seq_dat)
{
return(result)
}
print.loadData <- function(result, config)
{
cat('\n-------------------\n')
cat( 'Operation: loadData\n')
cat( '-------------------\n')
# cat('\nLoaded Sequences: Bases:\n')
# print(result$seq_dat@sread)
# cat('\nLoaded Sequences: Qualities:\n')
# print(result$seq_dat@quality@quality)
# cat('\nSummary:\n')
print(result$summary[,c('parameter', 'k_seqs', 'k_mean_length', 'k_mean_qual')])
invisible(result)
}
# result <- operation_function(all_results, config)
# result <- saveToDisk(result, config)
# result <- genReport(result, config)
# result <- genSummary(result, config)
# result <- print(result, config)
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