Read a FASTQ file

Parse a FASTQ file into a tidy tibble of sequencing reads.

Usage

mp_read_fastq(path, n = NULL)

Arguments

path

Character scalar. Path to a .fastq, .fq, .fastq.gz, or .fq.gz file.

n

Integer or NULL. If specified, only the first n records are returned.

Value

A molpath_parsed object whose data slot is a tibble with columns read_id, sequence, quality, and seq_length.

Details

Tries ShortRead::readFastq() first. Falls back to a base-R text parser that reads 4-line FASTQ records.

Examples

# \donttest{
fq_file <- system.file("extdata", "example.fastq", package = "molpathR")
if (nzchar(fq_file)) {
  result <- mp_read_fastq(fq_file, n = 100)
  print(result)
}
# }