Build a DRAGMAP v8 reference index — rdragmap_build

Runs the package-owned dragen-os hash-table generator once. The output directory must not already exist; its parent must exist. The returned index always contains the compressed hash table. It can also retain the much larger uncompressed hash and extension tables required for memory-mapped alignment.

Usage

rdragmap_build_index(
  reference_fasta,
  index_directory,
  executables = rdragmap_executables(),
  threads = 1L,
  hash_size = "0GB",
  memory_limit = "0GB",
  seed_length = 21L,
  seed_interval = 1,
  mask_bed = character(),
  decoys = character(),
  max_multi_base_seeds = integer(),
  write_uncompressed = FALSE
)

Arguments

reference_fasta: Absolute FASTA path.
index_directory: Absolute, not-yet-existing output directory.
executables: Explicit executable resolution from rdragmap_executables().
threads: Positive hash-generation worker count.
hash_size: Hash table size with B, KB, MB, or GB units. "0GB" requests the native automatic size calculation.
memory_limit: Hash generation memory limit in the same units. "0GB" requests the native automatic limit.
seed_length: Initial seed length.
seed_interval: Reference positions per seed.
mask_bed: Empty or one absolute BED path passed to --ht-mask-bed.
decoys: Empty or one absolute FASTA path passed to --ht-decoys.
max_multi_base_seeds: Empty or one non-negative maximum passed to --ht-max-multi-base-seeds.
write_uncompressed: Whether to retain hash_table.bin and extend_table.bin. These files require substantially more disk space but permit rdragmap_align(mmap_reference = TRUE) without decompressing the hash table for every alignment process.

Value

RdragmapIndexBuildResult 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)) built@index
#> <Rdragmap::RdragmapIndex>
#>  @ directory: chr "/tmp/RtmpjLi2BG/rdragmap-example-200f3739f8d8/index"
unlink(work, recursive = TRUE, force = TRUE)
# }