vcf/variant/record/info/field/value/array/values: Percent-decode stri…

…ng values

This changes the values iterator item from `&str` to `Cow<'_, str>`.

See #300.

noodles-bcf/src/record/codec/encoder/site/info/field/value.rs

@@ -1,4 +1,5 @@
 use std::{
+    borrow::Cow,
     cmp,
     io::{self, Write},
 };
@@ -273,7 +274,7 @@ where
 
 fn write_string_array_value<W>(
     writer: &mut W,
-    values: Box<dyn Values<'_, &str> + '_>,
+    values: Box<dyn Values<'_, Cow<'_, str>> + '_>,
 ) -> io::Result<()>
 where
     W: Write,
@@ -286,7 +287,7 @@ where
         }
 
         if let Some(t) = result? {
-            s.push_str(t);
+            s.push_str(&t);
         } else {
             s.push(MISSING_VALUE);
         }

noodles-bcf/src/record/info/field/value.rs

@@ -186,6 +186,8 @@ fn type_mismatch_error(value: Option<TypedValue>, expected: Type) -> io::Error {
 
 #[cfg(test)]
 mod tests {
+    use std::borrow::Cow;
+
     use super::*;
 
     #[test]
@@ -392,6 +394,9 @@ mod tests {
         fn t(mut src: &[u8], expected: &[Option<&str>]) {
             match read_value(&mut src, Number::Count(2), Type::String) {
                 Ok(Some(Value::Array(Array::String(values)))) => {
+                    let expected: Vec<_> =
+                        expected.iter().map(|value| value.map(Cow::from)).collect();
+
                     assert!(matches!(
                         values.iter().collect::<io::Result<Vec<_>>>(),
                         Ok(vs) if vs == expected

noodles-vcf/CHANGELOG.md

@@ -2,6 +2,15 @@
 
 ## Unreleased
 
+### Changed
+
+  * vcf/variant/record/info/field/value/array/values: Percent-decode string
+    values ([#300]).
+
+    This changes the values iterator item from `&str` to `Cow<'_, str>`.
+
+[#300]: https://github.com/zaeleus/noodles/issues/300
+
 ### Fixed
 
   * vcf/variant/record/info/field/value/array/values: Fix counting number of

noodles-vcf/src/io/reader/record_buf.rs

@@ -9,7 +9,7 @@ mod quality_score;
 mod reference_bases;
 mod reference_sequence_name;
 mod samples;
-mod value;
+pub(crate) mod value;
 
 use std::{error, fmt};
 

noodles-vcf/src/variant/record/info/field/value/array.rs

@@ -2,7 +2,7 @@
 
 mod values;
 
-use std::{fmt, io};
+use std::{borrow::Cow, fmt, io};
 
 pub use self::values::Values;
 
@@ -15,7 +15,7 @@ pub enum Array<'a> {
     /// A character array.
     Character(Box<dyn Values<'a, char> + 'a>),
     /// A string array.
-    String(Box<dyn Values<'a, &'a str> + 'a>),
+    String(Box<dyn Values<'a, Cow<'a, str>> + 'a>),
 }
 
 impl<'a> fmt::Debug for Array<'a> {

noodles-vcf/src/variant/record/info/field/value/array/values.rs

@@ -1,4 +1,6 @@
-use std::io;
+use std::{borrow::Cow, io};
+
+use crate::io::reader::record_buf::value::percent_decode;
 
 /// Variant record info field array value values.
 #[allow(clippy::len_without_is_empty)]
@@ -69,20 +71,20 @@ impl<'a> Values<'a, char> for &'a str {
     }
 }
 
-impl<'a> Values<'a, &'a str> for &'a str {
+impl<'a> Values<'a, Cow<'a, str>> for &'a str {
     fn len(&self) -> usize {
         count(self)
     }
 
-    fn iter(&self) -> Box<dyn Iterator<Item = io::Result<Option<&'a str>>> + '_> {
-        Box::new(
-            self.split(DELIMITER)
-                .map(|s| match s {
-                    MISSING => None,
-                    _ => Some(s),
-                })
-                .map(Ok),
-        )
+    fn iter(&self) -> Box<dyn Iterator<Item = io::Result<Option<Cow<'a, str>>>> + '_> {
+        Box::new(self.split(DELIMITER).map(|s| {
+            match s {
+                MISSING => Ok(None),
+                _ => percent_decode(s)
+                    .map(Some)
+                    .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e)),
+            }
+        }))
     }
 }
 
@@ -102,13 +104,20 @@ mod tests {
     use super::*;
 
     #[test]
-    fn test_string_values() {
+    fn test_string_values() -> io::Result<()> {
         let src = "";
-        let values: Box<dyn Values<'_, &'_ str>> = Box::new(src);
+        let values: Box<dyn Values<'_, Cow<'_, str>>> = Box::new(src);
         assert_eq!(values.len(), 0);
 
-        let src = "a,b";
-        let values: Box<dyn Values<'_, &'_ str>> = Box::new(src);
+        let src = "a,b%3Bc";
+        let values: Box<dyn Values<'_, Cow<'_, str>>> = Box::new(src);
         assert_eq!(values.len(), 2);
+
+        let mut iter = values.iter();
+        assert_eq!(iter.next().transpose()?, Some(Some(Cow::from("a"))));
+        assert_eq!(iter.next().transpose()?, Some(Some(Cow::from("b;c"))));
+        assert!(iter.next().transpose()?.is_none());
+
+        Ok(())
     }
 }

noodles-vcf/src/variant/record_buf/info/field/value/array.rs

@@ -1,4 +1,4 @@
-use std::io;
+use std::{borrow::Cow, io};
 
 /// A variant record info field array value.
 #[derive(Clone, Debug, PartialEq)]
@@ -45,14 +45,14 @@ where
     }
 }
 
-impl<'a> crate::variant::record::info::field::value::array::Values<'a, &'a str>
+impl<'a> crate::variant::record::info::field::value::array::Values<'a, Cow<'a, str>>
     for Values<'a, String>
 {
     fn len(&self) -> usize {
         self.0.len()
     }
 
-    fn iter(&self) -> Box<dyn Iterator<Item = io::Result<Option<&'a str>>> + '_> {
-        Box::new(self.0.iter().map(|s| Ok(s.as_deref())))
+    fn iter(&self) -> Box<dyn Iterator<Item = io::Result<Option<Cow<'a, str>>>> + '_> {
+        Box::new(self.0.iter().map(|s| Ok(s.as_deref().map(Cow::from))))
     }
 }