VCF File Writing

class Writer:
    def __init__(self, stream, template, lineterminator="\n"):
        """
        Initialize VCF writer.
        
        Parameters:
        - stream: file-like object, output stream
        - template: Reader object, provides header metadata and format
        - lineterminator: str, line ending character(s)
        """
        
    def write_record(self, record):
        """
        Write a variant record to the output file.
        
        Parameters:
        - record: _Record object to write
        """
        
    def flush(self):
        """Flush the output stream."""
        
    def close(self):
        """Close the output stream."""

class VCFWriter:
    """Alias for Writer class for backwards compatibility."""
    pass

import vcf

# Basic VCF writing
reader = vcf.Reader(filename='input.vcf')
writer = vcf.Writer(open('output.vcf', 'w'), reader)

for record in reader:
    # Optional: modify record
    if record.QUAL and record.QUAL > 30:
        writer.write_record(record)

writer.close()

# Writing filtered records
reader = vcf.Reader(filename='input.vcf')
with open('filtered.vcf', 'w') as output_file:
    writer = vcf.Writer(output_file, reader)
    
    for record in reader:
        # Filter by variant type
        if record.is_snp:
            writer.write_record(record)
    
    writer.flush()

# Copy with modifications
reader = vcf.Reader(filename='input.vcf')
writer = vcf.Writer(open('modified.vcf', 'w'), reader)

for record in reader:
    # Add INFO field
    record.INFO['PROCESSED'] = True
    writer.write_record(record)

writer.close()