INNER CODE UNIT · Python

convert_vcf

cbg-ethz/V-pipe · workflow/scripts/assemble_visualization_webpage.py:18

def convert_vcf(fname):
    """Convert VCF to JSON."""
    output = []

    if os.path.getsize(fname) == 0:
        print(f'Empty VCF: "{fname}"')
        return output

    print(f'Parsing VCF: "{fname}"')
    with open(fname) as fd:
        vcf_reader = vcf.Reader(fd)

        # check caller
        caller_source = vcf_reader.metadata["source"][0].lower()
        if caller_source.startswith("lofreq"):
            mode = "lofreq"
        elif caller_source.startswith("shorah"):
            mode = "shorah"

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