Function process_vcf 

pub fn process_vcf(
    file: &Path,
    reference_path: &Path,
    chr: String,
    region: ZeroBasedHalfOpen,
    min_gq: u16,
    mask_regions: Option<Arc<HashMap<String, Vec<(i64, i64)>>>>,
    allow_regions: Option<Arc<HashMap<String, Vec<(i64, i64)>>>>,
    position_allele_map: Arc<Mutex<HashMap<i64, (char, char)>>>,
) -> Result<(Vec<Variant>, Vec<usize>, Vec<String>, i64, MissingDataInfo, FilteringStats), VcfError>