def _add_necessary_columns(args, custom_columns):
    """
    Convenience function to tack on columns that are necessary for
    the functionality of the tool but yet have not been specifically
    requested by the user.
    """
    # we need to add the variant's chrom, start and gene if 
    # not already there.
    if custom_columns.find("gene") < 0:
        custom_columns += ", gene"
    if custom_columns.find("start") < 0:
        custom_columns += ", start"
    if custom_columns.find("alt") < 0:
        custom_columns += ", alt"
        
    return custom_columns