##INFO fields being dropped

[FlexLuthORF]

 cat 2202415007_hemi.vcf | head

/home/zmvanw01/projects/12-sample-comparison/hifiasm-path/geno_analysis/per_samp/2202415007/change_to_hemi/2202415007_hemi.vcf

=mpileup -B -a QS -Ou -f /home/zmvanw01/git_repos/immune_receptor_genomics/current/reference.fasta --threads 11 /home/zmvanw01/projects/12-sample-comparison/hifiasm-path/2202415007/2202415007.editRG.bam

##reference=file:///home/zmvanw01/git_repos/immune_receptor_genomics/current/reference.fasta

##contig=<ID=chr10,length=133797422>

##contig=<ID=chr11,length=135086622>

##contig=<ID=chr12,length=133275309>

##contig=<ID=chr13,length=114364328>

##contig=<ID=chr14,length=105480000>

##contig=<ID=chr15,length=101991189>

##contig=<ID=chr16,length=90338345>

(bcftools) [zmvanw01@bigdata change_to_hemi]$ cat ../2202415007.vcf | head

##fileformat=VCFv4.2

##FILTER=<ID=PASS,Description="All filters passed">

##bcftoolsVersion=1.19+htslib-1.19.1

##bcftoolsCommand=mpileup -B -a QS -Ou -f /home/zmvanw01/git_repos/immune_receptor_genomics/current/reference.fasta --threads 11 /home/zmvanw01/projects/12-sample-comparison/hifiasm-path/2202415007/2202415007.editRG.bam

##reference=file:///home/zmvanw01/git_repos/immune_receptor_genomics/current/reference.fasta

I am editing the below vcf file with the following script:

def change_genotypes(input_vcf, bedfile, output_path):
    vcf_reader = VCF(input_vcf, strict_gt=True)

    # Create a new VCF Writer using the input VCF as a template
    vcf_writer = Writer(output_path, vcf_reader)

    coords = read_bedfile(bedfile)

    for record in vcf_reader:
        for index, sample in enumerate(vcf_reader.samples):
            change_snp = False
            for chrom, start, end in coords:
                if record.CHROM != chrom:
                    continue
                if record.POS < start:
                    continue
                if record.POS > end:
                    continue
                change_snp = True
                break

            if change_snp:
                current_genotype = record.genotypes[index]
                if current_genotype is None or -1 in current_genotype:
                    record.genotypes[index] = [-1, -1, False]  # Set genotype to unknown
                elif 1 in current_genotype:
                    record.genotypes[index] = [-1, 1, False]  # Set genotype to ./1
                else:
                    record.genotypes[index] = [-1, 0, False]  # Set genotype to ./0
                
                # Reassign the genotypes field
                record.genotypes = record.genotypes

        vcf_writer.write_record(record)

    vcf_writer.close()
    vcf_reader.close()

I expect it to copy all ##info fields from the template to the new vcf, but it seems to truncate it? I am missing: ##fileformat=VCFv4.2

##FILTER=<ID=PASS,Description="All filters passed">

##bcftoolsVersion=1.19+htslib-1.19.1

##bcftoolsCommand

from the newly created file and it is causing downstream issues. It also seems to be placing the path to the new file right at the top with now ## before it.