INNER CODE UNIT · Python

concurrent_mode

PharmGKB/PharmCAT · preprocessor/pcat/preprocess.py:52

               concurrent_mode: bool = False, max_processes: int = 1, verbose: int = 0) -> list[Path]:
    """
    Normalize and prepare the input VCF for PharmCAT.
    """
    if len(vcf_files) == 0:
        raise ReportableException('Missing VCF input')

    # make sure we have samples
    if samples is None or len(samples) == 0:
        samples = util.read_vcf_samples(vcf_files[0], verbose=verbose)
    else:
        # make sure samples are in the vcf file
        vcf_samples = util.read_vcf_samples(vcf_files[0], verbose=verbose)
        for sample in samples:
            if sample not in vcf_samples:
                raise ReportableException('Sample "%s" not in VCF' % sample)

    basename = output_basename or input_basename

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