Translate genomic data between formats — genome

A lightweight composition of read_genome and write_genome. The input format is detected automatically and read with the corresponding format-specific reader. The resulting genome is then sent to the requested writer.

Usage

genome_translator(
  data,
  strata = NULL,
  output,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE
)

Arguments

data: A supported genomic file or object.
strata: Optional strata data or filename passed to readers and writers that support it. Default: strata = NULL.
output: Character vector naming one or more output formats.
filename: Optional output filename or prefix. Default: filename = NULL.
parallel.core: Number of processor cores passed to readers and writers that support parallel processing. Default: parallel.core = parallel::detectCores() - 1.
verbose: Logical. Display progress messages. Default: verbose = TRUE.

Value

Invisibly returns the result produced by write_genome(). Writers whose purpose is a file side effect may return NULL.

Details

Use a format-specific read_*() or write_*() function when you need arguments beyond their defaults.

Examples

if (FALSE) { # \dontrun{
genome_translator(
  data = "genomes.vcf",
  strata = "strata.tsv",
  output = "genepop",
  filename = "genomes.gen"
)
} # }