Project: s41467-025-62064-7 | Function: parse_column (python)

system: You are an expert Python programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow Python best practices and maintain consistent code style.
Return **only** the complete Python function code.

user: Complete this Python function:

**DESCRIPTION:** Implements the core variant calling algorithm that analyzes sequencing read alignments at a single genomic position to identify and quantify genetic variants (SNPs, insertions, deletions). This function performs the computational core of viral consensus generation by parsing pileup data, handling indels, and calculating allele frequencies.

**KEY TERMS:** {
  "alt_AF": "alternative allele frequency",
  "num_aln": "number of aligned reads",
  "COMB_allele": "combined allele counter",
  "ref_pos": "reference genome position",
  "major": "major (most frequent) allele",
  "n_del": "number of deleted nucleotides"
}

**CONTEXT CODE:**                    required = True)

parser.add_argument('-r', 
                    '--reference',
                    help='Reference genome fasta file',
                    type=str,
                   required = True)

parser.add_argument('-vf', 
                    '--variantfile',
                    help='Output path for variant tsv file',
                    type=str,
                   required = False)

parser.add_argument('-c', 
                    '--cores',
                    help='Number of cores to use for processing',
                    default=1,
                    type=int,
                   required = False)

parser.add_argument('-d', 
                    '--mindepth',
                    help='Minimal depth at which to not consider any alternative alleles',
                    default=30,
                    type=int,
                   required = False)

parser.add_argument('-af', 
                    '--minAF',
                    help='Minimal allele frequency to output',
                    default=0.1,
                    type=float,
                   required = False)

parser.add_argument('-k', 
                    '--keepindels',
                    help='Keep 1 and 2 nt indels',
                    action='store_true',
                   required = False)

def process_batch(start, stop, bamfile, reference):
    bamfile = pysam.AlignmentFile(bamfile, "rb")
    ref_name = bamfile.references[0]
    refseq = pysam.Fastafile(reference).fetch(ref_name)
    
    pileup = bamfile.pileup(contig=ref_name, start=start, stop=stop, ignore_orphans=False, min_mapping_quality=0, min_base_quality=0, truncate=True)
    
    return([parse_column(p.reference_pos, p.get_query_sequences(add_indels=True),p.get_num_aligned(), refseq) for p in pileup])

def parse_column(ref_pos, allele_list, num_aln, refseq):
    raise NotImplementedError("parse_column function has been masked for testing purposes")

def main():
    raise NotImplementedError("main function has been masked for testing purposes")

if __name__ == '__main__':
    main()

Complete the function implementation replacing "raise NotImplementedError".