Run a bcftools command and log stderr

Internal helper around sys::exec_internal() that:

• runs bcftools.path with the supplied args,

• appends stderr to a log file (if provided),

• optionally aborts on non-zero exit status.

Usage

bcftools_exec(
  bcftools.path,
  args,
  log.file = NULL,
  label = NULL,
  verbose = TRUE,
  fail_on_status = TRUE
)

Arguments

bcftools.path

(character) Path or name of the bcftools executable.

args

(character) Vector of arguments passed to bcftools.

log.file

(optional, character) Path to a log file. If not NULL, stderr is appended to this file with a small header. Default: log.file = NULL.

label

(optional, character) Short label used in the log header. Default: label = NULL.

verbose

(logical) If TRUE, the constructed command line is printed. Default: verbose = TRUE.

fail_on_status

(logical) If TRUE (default), a non-zero exit status triggers an error. If FALSE, the status is returned invisibly.

Default: fail_on_status = TRUE.

Value

Invisibly returns a list with:

• status – exit status (integer),

• stdout – character scalar with STDOUT,

• stderr – character scalar with STDERR.