varona.utils.cli_split

cli_main()

Entrypoint for the vcf_split CLI.

vcf_split_args() → ArgumentParser

Set up the argument parser for the vcf_split CLI.

usage: vcf_split
    [-h --help]
    [--log-level {debug,info,warning,error}]
    [--out-dir OUT_DIR]
    [--compress]
    (--chunk-size CHUNK_SIZE | --n-chunks N_CHUNKS)
    in_vcf

Split a VCF file into smaller pieces.

positional arguments:
  in_vcf                The VCF file to split.

options:
  -h, --help            show this help message and exit
  --log-level {debug,info,warning,error}
                        Set the logging level (default: WARNING)
  --out-dir OUT_DIR     The directory to save the split VCF files.
  --compress            Whether to compress the output files.
  --chunk-size CHUNK_SIZE
                        The number of records per chunk.
  --n-chunks N_CHUNKS   The number of chunks to split the VCF into.