Ligate ordered GLIMPSE2 chunk outputs — rglimpse2

Invokes GLIMPSE2_ligate once. The input list must contain exactly one existing absolute VCF/BCF path per line in chromosome order. Blank lines and surrounding whitespace are rejected because the native reader treats them as part of a path.

Usage

rglimpse2_ligate(
  input_list,
  output_bcf,
  executable,
  seed,
  threads = 1L,
  log = character()
)

Arguments

input_list: Absolute text-file path containing ordered chunk paths.
output_bcf: Absolute output .bcf, .vcf, or .vcf.gz path.
executable: Absolute GLIMPSE2_ligate path.
seed: Non-negative random seed.
threads: Positive worker count.
log: Empty or one absolute log output path.

Value

RGlimpse2RunResult or an RGlimpse2ErrorValue.