pub mod value;
use std::{io, mem, ops::Range, str};
use noodles_vcf::{
self as vcf,
header::record::value::map::format::{self, Number},
variant::record::samples::{
keys::key,
series::{value::Array, Value},
},
};
use crate::record::value::{array::Values, read_type, read_value, Type};
pub struct Series<'r> {
id: usize,
ty: Type,
src: &'r [u8],
}
impl<'r> Series<'r> {
pub fn name<'h>(&self, header: &'h vcf::Header) -> io::Result<&'h str> {
header
.string_maps()
.strings()
.get_index(self.id)
.ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "invalid string map ID"))
}
fn len(&self) -> usize {
match self.ty {
Type::Int8(len) => len,
Type::Int16(len) => len,
Type::Int32(len) => len,
Type::Float(len) => len,
Type::String(len) => len,
}
}
pub fn get(&self, header: &vcf::Header, i: usize) -> Option<Option<io::Result<Value<'r>>>> {
let name = match self.name(header) {
Ok(name) => name,
Err(e) => return Some(Some(Err(e))),
};
if name == key::GENOTYPE {
match self.ty {
Type::Int8(len) => return get_genotype_value(self.src, len, i),
_ => todo!("unhandled type"),
}
}
let (number, ty) = header
.formats()
.get(name)
.map(|format| (format.number(), format.ty()))
.expect("missing type definition");
let value = match (number, ty, self.ty) {
(Number::Count(0), _, _) => todo!("invalid number for type"),
(_, _, Type::Int8(0) | Type::Int16(0) | Type::Int32(0) | Type::Float(0)) => {
return Some(Some(Err(io::Error::new(
io::ErrorKind::InvalidData,
"invalid length",
))));
}
(Number::Count(1), format::Type::Integer, Type::Int8(len)) => {
get_i8_value(self.src, len, i)
}
(Number::Count(1), format::Type::Integer, Type::Int16(len)) => {
get_i16_value(self.src, len, i)
}
(Number::Count(1), format::Type::Integer, Type::Int32(len)) => {
get_i32_value(self.src, len, i)
}
(Number::Count(1), format::Type::Float, Type::Float(len)) => {
get_f32_value(self.src, len, i)
}
(Number::Count(1), format::Type::Character, Type::String(len)) => {
get_char_value(self.src, len, i)
}
(Number::Count(1), format::Type::String, Type::String(len)) => {
get_string_value(self.src, len, i)
}
(_, format::Type::Integer, Type::Int8(len)) => get_i8_array_value(self.src, len, i),
(_, format::Type::Integer, Type::Int16(len)) => get_i16_array_value(self.src, len, i),
(_, format::Type::Integer, Type::Int32(len)) => get_i32_array_value(self.src, len, i),
(_, format::Type::Float, Type::Float(len)) => get_f32_array_value(self.src, len, i),
(_, format::Type::Character, Type::String(len)) => {
get_char_array_value(self.src, len, i)
}
(_, format::Type::String, Type::String(len)) => {
get_string_array_value(self.src, len, i)
}
_ => todo!("unhandled type"),
};
match value {
Some(Some(value)) => Some(Some(Ok(value))),
Some(None) => Some(None),
None => None,
}
}
}
impl<'r> vcf::variant::record::samples::Series for Series<'r> {
fn name<'a, 'h: 'a>(&'a self, header: &'h vcf::Header) -> io::Result<&'a str> {
header
.string_maps()
.strings()
.get_index(self.id)
.ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "invalid string map ID"))
}
fn get<'a, 'h: 'a>(
&'a self,
header: &'h vcf::Header,
i: usize,
) -> Option<Option<io::Result<Value<'a>>>> {
self.get(header, i)
}
fn iter<'a, 'h: 'a>(
&'a self,
header: &'h vcf::Header,
) -> Box<dyn Iterator<Item = io::Result<Option<Value<'a>>>> + 'a> {
Box::new((0..self.len()).map(|i| {
self.get(header, i)
.ok_or_else(|| io::Error::from(io::ErrorKind::InvalidData))?
.transpose()
}))
}
}
pub(super) fn read_series<'a>(src: &mut &'a [u8], sample_count: usize) -> io::Result<Series<'a>> {
fn size_of(ty: Type) -> usize {
match ty {
Type::Int8(n) => mem::size_of::<i8>() * n,
Type::Int16(n) => mem::size_of::<i16>() * n,
Type::Int32(n) => mem::size_of::<i32>() * n,
Type::Float(n) => mem::size_of::<f32>() * n,
Type::String(n) => mem::size_of::<u8>() * n,
}
}
let id = read_string_map_index(src)?;
let ty = read_type(src)?.expect("invalid type");
let len = size_of(ty) * sample_count;
let (buf, rest) = src.split_at(len);
*src = rest;
Ok(Series { id, ty, src: buf })
}
fn read_string_map_index(src: &mut &[u8]) -> io::Result<usize> {
match read_value(src)?.and_then(|v| v.as_int()) {
Some(i) => usize::try_from(i).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e)),
None => Err(io::Error::new(
io::ErrorKind::InvalidData,
"invalid string map index",
)),
}
}
fn range<N>(i: usize, len: usize) -> Range<usize> {
let size = mem::size_of::<N>();
let start = size * i * len;
let end = start + size * len;
start..end
}
fn get_i8_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
use crate::record::codec::value::Int8;
let src = src.get(range::<i8>(i, len))?;
let value = match Int8::from(src[0] as i8) {
Int8::Value(n) => Some(Value::Integer(i32::from(n))),
Int8::Missing => None,
Int8::EndOfVector | Int8::Reserved(_) => todo!(),
};
Some(value)
}
fn get_i8_array_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
let src = src.get(range::<i8>(i, len))?;
let values = Values::<'_, i8>::new(src);
Some(Some(Value::Array(Array::Integer(Box::new(values)))))
}
fn get_i16_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
use crate::record::codec::value::Int16;
let src = src.get(range::<i16>(i, len))?;
let value = match Int16::from(i16::from_le_bytes(src.try_into().unwrap())) {
Int16::Value(n) => Some(Value::Integer(i32::from(n))),
Int16::Missing => None,
Int16::EndOfVector | Int16::Reserved(_) => todo!(),
};
Some(value)
}
fn get_i16_array_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
let src = src.get(range::<i16>(i, len))?;
let values = Values::<'_, i16>::new(src);
Some(Some(Value::Array(Array::Integer(Box::new(values)))))
}
fn get_i32_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
use crate::record::codec::value::Int32;
let src = src.get(range::<i32>(i, len))?;
let value = match Int32::from(i32::from_le_bytes(src.try_into().unwrap())) {
Int32::Value(n) => Some(Value::Integer(n)),
Int32::Missing => None,
Int32::EndOfVector | Int32::Reserved(_) => todo!(),
};
Some(value)
}
fn get_i32_array_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
let src = src.get(range::<i32>(i, len))?;
let values = Values::<'_, i32>::new(src);
Some(Some(Value::Array(Array::Integer(Box::new(values)))))
}
fn get_f32_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
use crate::record::codec::value::Float;
let src = src.get(range::<f32>(i, len))?;
let value = match Float::from(f32::from_le_bytes(src.try_into().unwrap())) {
Float::Value(n) => Some(Value::Float(n)),
Float::Missing => None,
Float::EndOfVector | Float::Reserved(_) => todo!(),
};
Some(value)
}
fn get_f32_array_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
let src = src.get(range::<f32>(i, len))?;
let values = Values::<'_, f32>::new(src);
Some(Some(Value::Array(Array::Float(Box::new(values)))))
}
fn get_string(src: &[u8], len: usize, i: usize) -> Option<&str> {
const NUL: u8 = 0x00;
let src = src.get(range::<u8>(i, len))?;
let src = match src.iter().position(|&b| b == NUL) {
Some(i) => &src[..i],
None => src,
};
Some(
str::from_utf8(src)
.map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
.unwrap(), )
}
fn get_char_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
const MISSING: char = '.';
let s = get_string(src, len, i)?;
let c = s.chars().next().unwrap();
match c {
MISSING => Some(None),
_ => Some(Some(Value::Character(c))),
}
}
fn get_char_array_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
let s = get_string(src, len, i)?;
Some(Some(Value::Array(Array::Character(Box::new(s)))))
}
fn get_string_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
const MISSING: &str = ".";
match get_string(src, len, i)? {
MISSING => Some(None),
s => Some(Some(Value::String(s))),
}
}
fn get_string_array_value(src: &[u8], len: usize, i: usize) -> Option<Option<Value<'_>>> {
let s = get_string(src, len, i)?;
Some(Some(Value::Array(Array::String(Box::new(s)))))
}
fn get_genotype_value(src: &[u8], len: usize, i: usize) -> Option<Option<io::Result<Value<'_>>>> {
use self::value::Genotype;
let src = src.get(range::<i8>(i, len))?;
Some(Some(Ok(Value::Genotype(Box::new(Genotype::new(src))))))
}
#[cfg(test)]
mod tests {
use noodles_vcf::header::{record::value::Map, StringMaps};
use super::*;
const NAME: &str = "value";
fn build_header_with_format<I>(name: I, number: Number, ty: format::Type) -> vcf::Header
where
I: Into<String>,
{
let mut header = vcf::Header::builder()
.add_format(
name,
Map::builder()
.set_number(number)
.set_type(ty)
.set_description("")
.build()
.unwrap(),
)
.build();
*header.string_maps_mut() = StringMaps::try_from(&header).unwrap();
header
}
#[test]
fn test_get_with_int8_values() {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: Option<i32>) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Integer(n)) => Some(n),
Some(_) => panic!(),
None => None,
};
assert_eq!(actual, expected);
}
let header = build_header_with_format(NAME, Number::Count(1), format::Type::Integer);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x05, 0x08, 0x80, ];
let series = Series {
id,
ty: Type::Int8(1),
src,
};
t(&series, &header, 0, Some(5));
t(&series, &header, 1, Some(8));
t(&series, &header, 2, None);
assert!(series.get(&header, 3).is_none());
}
#[test]
fn test_get_with_int8_array_values() {
fn t(
series: &Series<'_>,
header: &vcf::Header,
i: usize,
expected: Option<&[Option<i32>]>,
) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Array(Array::Integer(values))) => {
Some(values.iter().collect::<Result<Vec<_>, _>>().unwrap())
}
Some(_) => panic!(),
None => None,
};
assert_eq!(actual.as_deref(), expected);
}
let header = build_header_with_format(NAME, Number::Count(2), format::Type::Integer);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x05, 0x08, 0x0d, 0x80, 0x15, 0x81, 0x80, 0x81, ];
let series = Series {
id,
ty: Type::Int8(2),
src,
};
t(&series, &header, 0, Some(&[Some(5), Some(8)]));
t(&series, &header, 1, Some(&[Some(13), None]));
t(&series, &header, 2, Some(&[Some(21)]));
t(&series, &header, 3, Some(&[None])); assert!(series.get(&header, 4).is_none());
}
#[test]
fn test_get_with_int16_values() {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: Option<i32>) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Integer(n)) => Some(n),
Some(_) => panic!(),
None => None,
};
assert_eq!(actual, expected);
}
let header = build_header_with_format(NAME, Number::Count(1), format::Type::Integer);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x05, 0x00, 0x08, 0x00, 0x00, 0x80, ];
let series = Series {
id,
ty: Type::Int16(1),
src,
};
t(&series, &header, 0, Some(5));
t(&series, &header, 1, Some(8));
t(&series, &header, 2, None);
assert!(series.get(&header, 3).is_none());
}
#[test]
fn test_get_with_int16_array_values() {
fn t(
series: &Series<'_>,
header: &vcf::Header,
i: usize,
expected: Option<&[Option<i32>]>,
) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Array(Array::Integer(values))) => {
Some(values.iter().collect::<Result<Vec<_>, _>>().unwrap())
}
Some(_) => panic!(),
None => None,
};
assert_eq!(actual.as_deref(), expected);
}
let header = build_header_with_format(NAME, Number::Count(2), format::Type::Integer);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x05, 0x00, 0x08, 0x00, 0x0d, 0x00, 0x00, 0x80, 0x15, 0x00, 0x01, 0x80, 0x00, 0x80, 0x01, 0x80, ];
let series = Series {
id,
ty: Type::Int16(2),
src,
};
t(&series, &header, 0, Some(&[Some(5), Some(8)]));
t(&series, &header, 1, Some(&[Some(13), None]));
t(&series, &header, 2, Some(&[Some(21)]));
t(&series, &header, 3, Some(&[None])); assert!(series.get(&header, 4).is_none());
}
#[test]
fn test_get_with_int32_values() {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: Option<i32>) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Integer(n)) => Some(n),
Some(_) => panic!(),
None => None,
};
assert_eq!(actual, expected);
}
let header = build_header_with_format(NAME, Number::Count(1), format::Type::Integer);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x05, 0x00, 0x00, 0x00, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x80, ];
let series = Series {
id,
ty: Type::Int32(1),
src,
};
t(&series, &header, 0, Some(5));
t(&series, &header, 1, Some(8));
t(&series, &header, 2, None);
assert!(series.get(&header, 3).is_none());
}
#[test]
fn test_get_with_int32_array_values() {
fn t(
series: &Series<'_>,
header: &vcf::Header,
i: usize,
expected: Option<&[Option<i32>]>,
) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Array(Array::Integer(values))) => {
Some(values.iter().collect::<Result<Vec<_>, _>>().unwrap())
}
Some(_) => panic!(),
None => None,
};
assert_eq!(actual.as_deref(), expected);
}
let header = build_header_with_format(NAME, Number::Count(2), format::Type::Integer);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x05, 0x00, 0x00, 0x00, 0x08, 0x00, 0x00, 0x00, 0x0d, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x80, 0x15, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x80, 0x00, 0x00, 0x00, 0x80, 0x01, 0x00, 0x00, 0x80, ];
let series = Series {
id,
ty: Type::Int32(2),
src,
};
t(&series, &header, 0, Some(&[Some(5), Some(8)]));
t(&series, &header, 1, Some(&[Some(13), None]));
t(&series, &header, 2, Some(&[Some(21)]));
t(&series, &header, 3, Some(&[None])); assert!(series.get(&header, 4).is_none());
}
#[test]
fn test_get_with_float_values() {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: Option<f32>) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Float(n)) => Some(n),
Some(_) => panic!(),
None => None,
};
assert_eq!(actual, expected);
}
let header = build_header_with_format(NAME, Number::Count(1), format::Type::Float);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x80, 0x3f, 0x01, 0x00, 0x80, 0x7f, ];
let series = Series {
id,
ty: Type::Float(1),
src,
};
t(&series, &header, 0, Some(0.0));
t(&series, &header, 1, Some(1.0));
t(&series, &header, 2, None);
assert!(series.get(&header, 3).is_none());
}
#[test]
fn test_get_with_float_array_values() {
fn t(
series: &Series<'_>,
header: &vcf::Header,
i: usize,
expected: Option<&[Option<f32>]>,
) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Array(Array::Float(values))) => {
Some(values.iter().collect::<Result<Vec<_>, _>>().unwrap())
}
Some(_) => panic!(),
None => None,
};
assert_eq!(actual.as_deref(), expected);
}
let header = build_header_with_format(NAME, Number::Count(2), format::Type::Float);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x80, 0x3f, 0x00, 0x00, 0x00, 0x00, 0x01, 0x00, 0x80, 0x7f, 0x00, 0x00, 0x00, 0x00, 0x02, 0x00, 0x80, 0x7f, 0x01, 0x00, 0x80, 0x7f, 0x02, 0x00, 0x80, 0x7f, ];
let series = Series {
id,
ty: Type::Float(2),
src,
};
t(&series, &header, 0, Some(&[Some(0.0), Some(1.0)]));
t(&series, &header, 1, Some(&[Some(0.0), None]));
t(&series, &header, 2, Some(&[Some(0.0)]));
t(&series, &header, 3, Some(&[None])); assert!(series.get(&header, 4).is_none());
}
#[test]
fn test_get_with_character_value() {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: Option<char>) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::Character(c)) => Some(c),
Some(_) => panic!(),
None => None,
};
assert_eq!(actual, expected);
}
let header = build_header_with_format(NAME, Number::Count(1), format::Type::Character);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
b'n', b'd', b'.', ];
let series = Series {
id,
ty: Type::String(1),
src,
};
t(&series, &header, 0, Some('n'));
t(&series, &header, 1, Some('d'));
t(&series, &header, 2, None);
assert!(series.get(&header, 3).is_none());
}
#[test]
fn test_get_with_character_array_value() {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: &[Option<char>]) {
match series.get(header, i).unwrap().unwrap().unwrap() {
Value::Array(Array::Character(values)) => {
assert_eq!(
values.iter().collect::<Result<Vec<_>, _>>().unwrap(),
expected,
);
}
_ => panic!(),
}
}
let header = build_header_with_format(NAME, Number::Count(2), format::Type::Character);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
b'n', b',', b'd', b'n', b',', b'.', b'n', 0x00, 0x00, ];
let series = Series {
id,
ty: Type::String(3),
src,
};
t(&series, &header, 0, &[Some('n'), Some('d')]);
t(&series, &header, 1, &[Some('n'), None]);
t(&series, &header, 2, &[Some('n')]);
assert!(series.get(&header, 3).is_none());
}
#[test]
fn test_get_with_string_value() {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: Option<&str>) {
let actual = match series.get(header, i).unwrap().transpose().unwrap() {
Some(Value::String(s)) => Some(s),
Some(_) => panic!(),
None => None,
};
assert_eq!(actual, expected);
}
let header = build_header_with_format(NAME, Number::Count(1), format::Type::String);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
b'n', 0x00, 0x00, 0x00, b'n', b'd', b'l', b's', b'.', 0x00, 0x00, 0x00, ];
let series = Series {
id,
ty: Type::String(4),
src,
};
t(&series, &header, 0, Some("n"));
t(&series, &header, 1, Some("ndls"));
t(&series, &header, 2, None);
assert!(series.get(&header, 3).is_none());
}
#[test]
fn test_get_with_string_array_value() -> Result<(), Box<dyn std::error::Error>> {
fn t(series: &Series<'_>, header: &vcf::Header, i: usize, expected: &[Option<&str>]) {
match series.get(header, i).unwrap().unwrap().unwrap() {
Value::Array(Array::String(values)) => {
assert_eq!(
values.iter().collect::<Result<Vec<_>, _>>().unwrap(),
expected,
);
}
_ => panic!(),
}
}
let header = build_header_with_format(NAME, Number::Count(2), format::Type::String);
let id = header.string_maps().strings().get_index_of(NAME).unwrap();
let src = &[
b'n', 0x00, 0x00, 0x00, b'n', b',', b'l', 0x00, b'n', b',', b'l', b's', ];
let series = Series {
id,
ty: Type::String(4),
src,
};
t(&series, &header, 0, &[Some("n")]);
t(&series, &header, 1, &[Some("n"), Some("l")]);
t(&series, &header, 2, &[Some("n"), Some("ls")]);
assert!(series.get(&header, 3).is_none());
Ok(())
}
}