Phase and impute one GLIMPSE2 chunk from genotype likelihoods

Invokes GLIMPSE2_phase once against a binary reference chunk. RGlimpse2 currently requires one internal phase thread so a fixed seed is not coupled to worker scheduling; parallelism belongs across independent chunks.

Usage

rglimpse2_phase(
  input_gl,
  reference_bin,
  output_bcf,
  executable,
  seed,
  threads = 1L,
  sample_ploidy = character(),
  input_field = c("PL", "GL"),
  burnin = 5L,
  main = 15L,
  ne = 100000L,
  pbwt_depth = 12L,
  pbwt_modulo_cm = 0.1,
  k_init = 1000L,
  k_pbwt = 2000L,
  impute_reference_only_variants = FALSE,
  use_gl_indels = FALSE,
  log = character()
)

Arguments

input_gl

Absolute VCF/BCF genotype-likelihood path.

reference_bin

Absolute GLIMPSE2 binary reference path.

output_bcf

Absolute .bcf, .vcf, or .vcf.gz output path.

executable

Absolute selected GLIMPSE2_phase path.

seed

Non-negative random seed.

threads

Must be 1L under the current deterministic contract.

sample_ploidy

Empty or one absolute sample/ploidy table path.

input_field

Genotype likelihood field, "PL" or "GL".

burnin

Number of burn-in iterations.

main

Number of main iterations, at most 15.

ne

Positive effective diploid population size.

pbwt_depth

Positive PBWT neighbour depth.

pbwt_modulo_cm

Positive PBWT selection spacing in cM.

k_init, k_pbwt

Positive conditioning-state limits.

impute_reference_only_variants

Whether to admit sporadically absent target likelihood records from the reference.

use_gl_indels

Whether to consume input likelihoods at indels rather than use the default flat-likelihood scaffold behavior.

log

Empty or one absolute log output path.

Value

RGlimpse2RunResult or an RGlimpse2ErrorValue.