#' Removes perimer-dimer sequences (based on sequence length)
#' @inheritParams applyOperation
#' @export
primerDimer <- 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$base_for_names, op_full_name)
dir.create(op_dir, showWarnings = FALSE, recursive = TRUE)
data_source_indx <- grep(op_args$data_source, names(all_results))
stopifnot(length(data_source_indx) == 1)
seq_dat <- all_results[[data_source_indx]]$seq_dat
per_read_metrics <- data.frame(seq_len = width(seq_dat@sread))
threshold <- op_args$threshold
if (is.null(threshold))
{
threshold <- 80
}
trim_steps <- list(step1 = list(name = 'seq_len',
threshold = threshold,
comparator = `>=`,
breaks = c(Inf, 295, 100, 80, 50, 30, -Inf)
)
)
result <- list(trim_steps = trim_steps,
metrics = list(per_read_metrics = per_read_metrics))
kept_dat <- getKept(result, seq_dat=seq_dat)
class(result) <- 'primerDimer'
if (op_args$cache){
result$seq_dat <- kept_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)
}
saveToDisk.primerDimer <- function(result, config, seq_dat)
{
kept <- getKept(result, seq_dat)
trimmed <- getTrimmed(seq_dat = seq_dat, kept_dat = kept)
if (length(kept) > 0)
{
tmp_name <- file.path(result$config$op_dir,
paste(config$base_for_names, '_kept_', result$config$op_args$name, '.fastq', sep = ''))
writeFastq(kept, tmp_name, compress=F)
}
if (length(trimmed) > 0)
{
tmp_name <- file.path(result$config$op_dir,
paste(config$base_for_names, '_trimmed_', result$config$op_args$name, '.fastq', sep = ''))
writeFastq(trimmed, tmp_name, compress=F)
}
return(result)
}
computeMetrics.primerDimer <- function(result, config, seq_dat)
{
kept <- getKept(result, seq_dat)
trimmed <- getTrimmed(seq_dat = seq_dat, kept_dat = kept)
if (length(trimmed) < 5){
consMat <- NULL
} else {
consMat <- consensusMatrix(trimmed@sread)
}
result$metrics$consMat <- consMat[c(1:4,15),]
return(result)
}
print.primerDimer <- function(result, config)
{
cat('\n-------------------')
cat('\nOperation: primerDimer')
cat('\n-------------------')
cat('\nKept Sequences:\n')
print(result$summary[,c('parameter', 'k_seqs', 'k_mean_length', 'k_mean_qual')])
cat('\n-------------------')
cat('\nTrimmed Sequences:\n')
print(result$summary[,c('parameter', 't_seqs', 't_mean_length', 't_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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