Align FASTQ reads with a DRAGMAP v8 reference index

Runs the package-owned dragen-os executable once and writes SAM plus native mapping metrics beside output_sam. Paired input also writes native insert-size statistics. The wrapper preserves map/align order by default so that the native SAM ordering remains deterministic.

Usage

rdragmap_align(
  index,
  read1,
  output_sam,
  read2 = character(),
  executables = rdragmap_executables(),
  read_group_id = "1",
  sample_name = "none",
  threads = 1L,
  fastq_offset = 33L,
  enable_sampling = TRUE,
  preserve_order = TRUE,
  mmap_reference = FALSE
)

Arguments

index: A validated RdragmapIndex.
read1: Absolute first FASTQ path, optionally gzip-compressed.
output_sam: Absolute, not-yet-existing .sam output path.
read2: Empty or one absolute mate FASTQ path.
executables: Explicit executable resolution from rdragmap_executables().
read_group_id: Read-group identifier recorded in the SAM header.
sample_name: Read-group sample recorded in the SAM header.
threads: Positive mapper/aligner worker count.
fastq_offset: FASTQ quality offset, 33L or 64L.
enable_sampling: Whether the native program estimates paired-end insert-size parameters from the input.
preserve_order: Whether to preserve deterministic map/align order.
mmap_reference: Whether to memory-map the uncompressed hash, extension, and reference files. The index must have been built with write_uncompressed = TRUE or otherwise contain hash_table.bin and extend_table.bin.

Value

RdragmapAlignmentResult or an RdragmapErrorValue.

Examples

# \donttest{
work <- tempfile("rdragmap-example-")
dir.create(work)
built <- rdragmap_build_index(
  reference_fasta = system.file("extdata", "tiny.fasta", package = "Rdragmap"),
  index_directory = file.path(work, "index"),
  threads = 1L,
  hash_size = "16MB"
)
if (!rdragmap_is_error(built)) {
  aligned <- rdragmap_align(
    index = built@index,
    read1 = system.file("extdata", "one.fastq", package = "Rdragmap"),
    output_sam = file.path(work, "example.sam"),
    read_group_id = "tiny",
    sample_name = "tiny",
    threads = 1L,
    enable_sampling = FALSE
  )
  if (!rdragmap_is_error(aligned)) aligned@outputs
}
#> $sam
#> [1] "/tmp/RtmpjLi2BG/rdragmap-example-200f620a8dfe/example.sam"
#> 
#> $mapping_metrics
#> [1] "/tmp/RtmpjLi2BG/rdragmap-example-200f620a8dfe/example.mapping_metrics.csv"
#> 
unlink(work, recursive = TRUE, force = TRUE)
# }