Convert `.fastq` to `.bam` — fastq_to

This function converts a `.fastq` file to a `.bam` file using a dummy `.sam` format. It reads the `.fastq` file, extracts the sequence identifiers and sequences, and creates a dummy `.sam` file.

Usage

fastq_to_bam(
  fastq_file,
  patient_id,
  output_dir = tempdir(),
  sam_file = paste0(output_dir, "/", patient_id, ".sam"),
  reference = "chr1"
)

Arguments

fastq_file: A character string specifying the path to the `.fastq` file.
patient_id: A character string specifying the patient ID. This will be used as the base name for the output `.sam` file.
output_dir: A character string specifying the directory where the output `.sam` file will be saved. Default is a temporary directory.
sam_file: A character string specifying the path to the output `.sam` file.
reference: A character string specifying the reference sequence name. Default is "chr1".

Details

The function reads the `.fastq` file and extracts the sequence identifiers and sequences. It then creates a dummy `.sam` file with the following fields: - QNAME: Query name (read identifier) - FLAG: Bitwise flag (0 for unmapped) - RNAME: Reference sequence name - POS: Position on the reference sequence - MAPQ: Mapping quality (255 for unmapped) - CIGAR: CIGAR string (length of the sequence) - RNEXT: Reference name of the next read (dummy value "*") - PNEXT: Position of the next read (dummy value 0) - TLEN: Template length (dummy value 0) - SEQ: Sequence - QUAL: Quality scores

Examples

# Convert a `.fastq` file to a `.bam` file
output_dir <- tempdir()
n <- 2
read_length <- 8
patient_id <- "patient_123"
fastq_file <- file.path(output_dir, paste0(patient_id, ".fastq"))
fill_fastq(patient_id, output_dir, n, read_length)
#> File already exists. Appending reads to the existing file.
#> Populated /tmp/RtmpCk48DO/patient_123.fastq with 2 reads.
sam_file <- paste0(output_dir, "/", patient_id, ".sam")
fastq_to_bam(fastq_file, patient_id, output_dir, sam_file)
#> Dummy .sam file written to: /tmp/RtmpCk48DO/patient_123.sam