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vcf/io/writer/record/info: Write from Info trait
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@zaeleus
zaeleus committed Feb 28, 2024
1 parent 22a95a8 commit fe06468
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Showing 3 changed files with 47 additions and 33 deletions.
4 changes: 2 additions & 2 deletions noodles-vcf/src/io/writer.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -145,8 +145,8 @@ where
/// writer.write_record(&header, &record)?;
/// # Ok::<_, std::io::Error>(())
/// ```
pub fn write_record(&mut self, _: &Header, record: &RecordBuf) -> io::Result<()> {
write_record(&mut self.inner, record)
pub fn write_record(&mut self, header: &Header, record: &RecordBuf) -> io::Result<()> {
write_record(&mut self.inner, header, record)
}
}

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9 changes: 5 additions & 4 deletions noodles-vcf/src/io/writer/record.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,11 @@ use self::{
info::write_info, position::write_position, quality_score::write_quality_score,
reference_sequence_name::write_reference_sequence_name, samples::write_samples,
};
use crate::variant::RecordBuf;
use crate::{variant::RecordBuf, Header};

const MISSING: &[u8] = b".";

pub(super) fn write_record<W>(writer: &mut W, record: &RecordBuf) -> io::Result<()>
pub(super) fn write_record<W>(writer: &mut W, header: &Header, record: &RecordBuf) -> io::Result<()>
where
W: Write,
{
Expand All @@ -45,7 +45,7 @@ where
write_filters(writer, record.filters())?;

writer.write_all(DELIMITER)?;
write_info(writer, record.info())?;
write_info(writer, header, record.info())?;

if !record.samples().is_empty() {
writer.write_all(DELIMITER)?;
Expand All @@ -71,8 +71,9 @@ mod tests {
.set_reference_bases("A")
.build();

let header = Header::default();
let mut buf = Vec::new();
write_record(&mut buf, &record)?;
write_record(&mut buf, &header, &record)?;
assert_eq!(buf, b"sq0\t1\t.\tA\t.\t.\t.\t.\n");

Ok(())
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67 changes: 40 additions & 27 deletions noodles-vcf/src/io/writer/record/info.rs
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Original file line number Diff line number Diff line change
@@ -1,24 +1,28 @@
use std::io::{self, Write};

use super::MISSING;
use crate::variant::record_buf::{
info::field::{value::Array, Value},
Info,
use crate::{
variant::record::{
info::field::{value::Array, Value},
Info,
},
Header,
};

pub(super) fn write_info<W>(writer: &mut W, info: &Info) -> io::Result<()>
pub(super) fn write_info<W, I>(writer: &mut W, header: &Header, info: I) -> io::Result<()>
where
W: Write,
I: Info,
{
const DELIMITER: &[u8] = b";";
const SEPARATOR: &[u8] = b"=";

let info = info.as_ref();

if info.is_empty() {
writer.write_all(MISSING)?;
} else {
for (i, (key, value)) in info.iter().enumerate() {
for (i, result) in info.iter(header).enumerate() {
let (key, value) = result?;

if i > 0 {
writer.write_all(DELIMITER)?;
}
Expand All @@ -29,7 +33,7 @@ where
Some(Value::Flag) => {}
Some(v) => {
writer.write_all(SEPARATOR)?;
write_value(writer, v)?;
write_value(writer, &v)?;
}
None => {
writer.write_all(SEPARATOR)?;
Expand All @@ -55,12 +59,12 @@ where
Value::Character(c) => write!(writer, "{c}"),
Value::String(s) => writer.write_all(s.as_bytes()),
Value::Array(Array::Integer(values)) => {
for (i, v) in values.iter().enumerate() {
for (i, result) in values.iter().enumerate() {
if i > 0 {
writer.write_all(DELIMITER)?;
}

if let Some(n) = v {
if let Some(n) = result? {
write!(writer, "{n}")?;
} else {
writer.write_all(MISSING)?;
Expand All @@ -70,12 +74,12 @@ where
Ok(())
}
Value::Array(Array::Float(values)) => {
for (i, v) in values.iter().enumerate() {
for (i, result) in values.iter().enumerate() {
if i > 0 {
writer.write_all(DELIMITER)?;
}

if let Some(n) = v {
if let Some(n) = result? {
write!(writer, "{n}")?;
} else {
writer.write_all(MISSING)?;
Expand All @@ -85,12 +89,12 @@ where
Ok(())
}
Value::Array(Array::Character(values)) => {
for (i, v) in values.iter().enumerate() {
for (i, result) in values.iter().enumerate() {
if i > 0 {
writer.write_all(DELIMITER)?;
}

if let Some(c) = v {
if let Some(c) = result? {
write!(writer, "{c}")?;
} else {
writer.write_all(MISSING)?;
Expand All @@ -100,12 +104,12 @@ where
Ok(())
}
Value::Array(Array::String(values)) => {
for (i, v) in values.iter().enumerate() {
for (i, result) in values.iter().enumerate() {
if i > 0 {
writer.write_all(DELIMITER)?;
}

if let Some(s) = v {
if let Some(s) = result? {
writer.write_all(s.as_bytes())?;
} else {
writer.write_all(MISSING)?;
Expand All @@ -123,39 +127,48 @@ mod tests {

#[test]
fn test_write_info() -> io::Result<()> {
use crate::variant::record_buf::info::field::key;

fn t(buf: &mut Vec<u8>, info: &Info, expected: &[u8]) -> io::Result<()> {
use crate::variant::record_buf::{
info::field::{key, Value as ValueBuf},
Info as InfoBuf,
};

fn t(
buf: &mut Vec<u8>,
header: &Header,
info: &InfoBuf,
expected: &[u8],
) -> io::Result<()> {
buf.clear();
write_info(buf, info)?;
write_info(buf, header, info)?;
assert_eq!(buf, expected);
Ok(())
}

let header = Header::default();
let mut buf = Vec::new();

let info = Info::default();
t(&mut buf, &info, b".")?;
let info = InfoBuf::default();
t(&mut buf, &header, &info, b".")?;

let info = [(
String::from(key::SAMPLES_WITH_DATA_COUNT),
Some(Value::from(2)),
Some(ValueBuf::from(2)),
)]
.into_iter()
.collect();
t(&mut buf, &info, b"NS=2")?;
t(&mut buf, &header, &info, b"NS=2")?;

let info = [
(
String::from(key::SAMPLES_WITH_DATA_COUNT),
Some(Value::from(2)),
Some(ValueBuf::from(2)),
),
(String::from(key::IS_IN_DB_SNP), Some(Value::Flag)),
(String::from(key::IS_IN_DB_SNP), Some(ValueBuf::Flag)),
]
.into_iter()
.collect();

t(&mut buf, &info, b"NS=2;DB")?;
t(&mut buf, &header, &info, b"NS=2;DB")?;

Ok(())
}
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