VCF File Parsing

class Reader:
    def __init__(self, fsock=None, filename=None, compressed=None, 
                 prepend_chr=False, strict_whitespace=False, encoding='ascii'):
        """
        Initialize VCF reader from file or stream.
        
        Parameters:
        - fsock: file-like object, open file handle
        - filename: str, path to VCF file
        - compressed: bool, whether file is gzip compressed (auto-detected)
        - prepend_chr: bool, add 'chr' prefix to chromosome names
        - strict_whitespace: bool, strict whitespace parsing
        - encoding: str, file encoding (default 'ascii')
        """
        
    def __iter__(self):
        """Iterator interface returning _Record objects."""
        
    def __next__(self):
        """Get next variant record (Python 3.x iterator protocol)."""
        
    def next(self):
        """Get next variant record (Python 2.x compatibility)."""
        
    def fetch(self, chrom, start=None, end=None):
        """
        Tabix-based region queries (requires pysam and indexed file).
        
        Parameters:
        - chrom: str, chromosome name
        - start: int, start position (0-based, optional)
        - end: int, end position (0-based, optional)
        
        Returns:
        Iterator of _Record objects in region
        """

# Reader properties
metadata: dict  # Complete header metadata (OrderedDict)
infos: dict  # INFO field definitions (OrderedDict of _Info objects)
filters: dict  # FILTER field definitions (OrderedDict of _Filter objects)
formats: dict  # FORMAT field definitions (OrderedDict of _Format objects)
alts: dict  # ALT field definitions (OrderedDict of _Alt objects)
contigs: dict  # Contig information (OrderedDict of _Contig objects)
samples: list  # Sample names from header
filename: str  # Input filename if provided
encoding: str  # File encoding used

class VCFReader:
    """Alias for Reader class for backwards compatibility."""
    pass

import vcf

# Basic file reading
reader = vcf.Reader(filename='variants.vcf')
for record in reader:
    print(f"Variant at {record.CHROM}:{record.POS}")

# Reading from compressed file
reader = vcf.Reader(filename='variants.vcf.gz')

# Reading from file handle
with open('variants.vcf', 'r') as f:
    reader = vcf.Reader(fsock=f)
    
# Access header information
reader = vcf.Reader(filename='variants.vcf')
print("Samples:", reader.samples)
print("INFO fields:", list(reader.infos.keys()))

# Tabix region queries (requires pysam and indexed file)
reader = vcf.Reader(filename='variants.vcf.gz')
for record in reader.fetch('chr1', 1000000, 2000000):
    print(f"Variant in region: {record.CHROM}:{record.POS}")

class _Info:
    """INFO field metadata."""
    id: str
    num: str
    type: str
    desc: str
    source: str
    version: str

class _Filter:
    """FILTER field metadata."""
    id: str
    desc: str

class _Format:
    """FORMAT field metadata."""
    id: str
    num: str
    type: str
    desc: str

class _Contig:
    """Contig metadata."""
    id: str
    length: int

class _Alt:
    """ALT field metadata."""
    id: str
    desc: str