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mod record;
mod string_map;
mod value;
use std::{
convert::TryFrom,
ffi::CString,
io::{self, Write},
};
use byteorder::{LittleEndian, WriteBytesExt};
use noodles_bgzf as bgzf;
use noodles_vcf as vcf;
use super::{header::StringMap, MAGIC_NUMBER};
const MAJOR: u8 = 2;
const MINOR: u8 = 2;
pub struct Writer<W>
where
W: Write,
{
inner: bgzf::Writer<W>,
}
impl<W> Writer<W>
where
W: Write,
{
pub fn new(writer: W) -> Self {
Self {
inner: bgzf::Writer::new(writer),
}
}
pub fn get_ref(&self) -> &W {
self.inner.get_ref()
}
pub fn try_finish(&mut self) -> io::Result<()> {
self.inner.try_finish()
}
pub fn write_file_format(&mut self) -> io::Result<()> {
self.inner.write_all(MAGIC_NUMBER)?;
self.inner.write_u8(MAJOR)?;
self.inner.write_u8(MINOR)?;
Ok(())
}
pub fn write_header(&mut self, header: &vcf::Header) -> io::Result<()> {
let raw_header = header.to_string();
let c_raw_header =
CString::new(raw_header).map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
let text = c_raw_header.as_bytes_with_nul();
let l_text = u32::try_from(text.len())
.map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
self.inner.write_u32::<LittleEndian>(l_text)?;
self.inner.write_all(text)?;
Ok(())
}
pub fn write_vcf_record(
&mut self,
header: &vcf::Header,
string_map: &StringMap,
record: &vcf::Record,
) -> io::Result<()> {
let mut site_buf = Vec::new();
record::write_site(&mut site_buf, header, string_map, record)?;
let l_shared = u32::try_from(site_buf.len())
.map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
let mut genotypes_buf = Vec::new();
if let Some(format) = record.format() {
record::write_genotypes(&mut genotypes_buf, string_map, format, record.genotypes())?;
};
let l_indiv = u32::try_from(genotypes_buf.len())
.map_err(|e| io::Error::new(io::ErrorKind::InvalidInput, e))?;
self.inner.write_u32::<LittleEndian>(l_shared)?;
self.inner.write_u32::<LittleEndian>(l_indiv)?;
self.inner.write_all(&site_buf)?;
self.inner.write_all(&genotypes_buf)?;
Ok(())
}
}
#[cfg(test)]
mod tests {
use crate::Reader;
use super::*;
#[test]
fn test_write_file_format() -> io::Result<()> {
let mut writer = Writer::new(Vec::new());
writer.write_file_format()?;
writer.try_finish()?;
let mut reader = Reader::new(writer.get_ref().as_slice());
let file_format = reader.read_file_format()?;
assert_eq!(file_format, (2, 2));
Ok(())
}
#[test]
fn test_write_header() -> io::Result<()> {
let mut writer = Writer::new(Vec::new());
writer.write_file_format()?;
let header = vcf::Header::default();
writer.write_header(&header)?;
writer.try_finish()?;
let mut reader = Reader::new(writer.get_ref().as_slice());
reader.read_file_format()?;
let actual = reader.read_header()?;
let expected = "##fileformat=VCFv4.3\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
assert_eq!(actual, expected);
Ok(())
}
}