Convert Local-Ancestry Tracts Format from Text to GDS — convert_txt_to

Converts ancestry-specific dosage/hapcount text files into a tracts GDS file.

Usage

convert_txt_to_gds(
  input_prefix,
  num_ancs,
  output_prefix = NULL,
  chunk_size = 1024L
)

Arguments

input_prefix: Character; input file prefix used to locate ancestry files. Expected files per ancestry k: <input_prefix>.anc{k}.dosage.txt(.gz) and <input_prefix>.anc{k}.hapcount.txt(.gz).
num_ancs: Integer; number of ancestral populations (must be > 1).
output_prefix: Character or NULL; output GDS prefix. If NULL (default), uses input_prefix.
chunk_size: Integer; number of variants processed per chunk. Default is 1024; higher values can improve speed but increase memory usage.

Value

Invisibly returns NULL. Writes <output_prefix>.gds.

Details

The generated GDS contains sample.id, variant metadata (snp.chromosome, snp.position, snp.id, snp.ref, snp.alt), and ancestry-specific nodes dosage/anc0..ancK and hapcount/anc0..ancK.