vcf/header/parser/record/value/map/other: Only parse Values field in …

…VCF 4.3+ META records
zaeleus · Sep 18, 2023 · 47715cd · 47715cd
1 parent f40d7a3
commit 47715cd
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Showing 3 changed files with 37 additions and 5 deletions.
diff --git a/noodles-vcf/CHANGELOG.md b/noodles-vcf/CHANGELOG.md
@@ -14,8 +14,8 @@
     When the input is VCF 4.2, this allows the `Child` or `Derived` field to
     act as the record ID in the value collection.
 
-  * vcf/header/parser/record/value/map/other: Only parse `Values` field in META
-    record.
+  * vcf/header/parser/record/value/map/other: Only parse `Values` field in VCF
+    4.3+ META records.
 
 [#201]: https://github.com/zaeleus/noodles/issues/201
 [#203]: https://github.com/zaeleus/noodles/issues/203

diff --git a/noodles-vcf/src/header/parser/record/value.rs b/noodles-vcf/src/header/parser/record/value.rs
@@ -181,7 +181,7 @@ pub(super) fn parse_value(
             .map_err(ParseError::InvalidContig),
         Key::Other(k) => {
             let v = if k.as_ref() == META {
-                map::other::parse_meta(src)
+                map::other::parse_meta(src, file_format)
                     .map(Value::from)
                     .map_err(|e| ParseError::InvalidOtherMap(k.clone(), e))?
             } else if k.as_ref() == PEDIGREE {

diff --git a/noodles-vcf/src/header/parser/record/value/map/other.rs b/noodles-vcf/src/header/parser/record/value/map/other.rs
@@ -103,8 +103,12 @@ pub fn parse_other(src: &mut &[u8]) -> Result<(String, Map<Other>), ParseError>
     ))
 }
 
-pub fn parse_meta(src: &mut &[u8]) -> Result<(String, Map<Other>), ParseError> {
+pub fn parse_meta(
+    src: &mut &[u8],
+    file_format: FileFormat,
+) -> Result<(String, Map<Other>), ParseError> {
     const VALUES: &str = "Values";
+    const VCF_4_3: FileFormat = FileFormat::new(4, 3);
 
     super::consume_prefix(src).map_err(|e| ParseError::new(None, ParseErrorKind::InvalidMap(e)))?;
 
@@ -119,7 +123,7 @@ pub fn parse_meta(src: &mut &[u8]) -> Result<(String, Map<Other>), ParseError> {
         match tag {
             tag::ID => parse_id(src, &id).and_then(|v| try_replace(&mut id, &None, tag::ID, v))?,
             Tag::Other(t) => {
-                if t == VALUES {
+                if file_format >= VCF_4_3 && t == VALUES {
                     parse_values(src, &id, &t)
                         .and_then(|value| try_insert(&mut other_fields, &id, t, value))?;
                 } else {
@@ -302,6 +306,34 @@ mod tests {
         assert_eq!(parse_other(&mut src), Ok(expected));
     }
 
+    #[test]
+    fn test_parse_meta() -> Result<(), Box<dyn std::error::Error>> {
+        const VCF_4_2: FileFormat = FileFormat::new(4, 2);
+        const VCF_4_3: FileFormat = FileFormat::new(4, 3);
+
+        let mut src = &b"<ID=Assay,Values=[WholeGenome, Exome]>"[..];
+        assert_eq!(
+            parse_meta(&mut src, VCF_4_3),
+            Ok((
+                String::from("Assay"),
+                Map::<Other>::builder()
+                    .insert("Values".parse()?, "[WholeGenome, Exome]")
+                    .build()?
+            ))
+        );
+
+        let mut src = &b"<ID=Assay,Values=[WholeGenome, Exome]>"[..];
+        assert!(matches!(
+            parse_meta(&mut src, VCF_4_2),
+            Err(ParseError {
+                id,
+                kind: ParseErrorKind::InvalidKey(_)
+            }) if id == Some(String::from("Assay"))
+        ));
+
+        Ok(())
+    }
+
     #[test]
     fn test_parse_pedigree() -> Result<(), Box<dyn std::error::Error>> {
         const VCF_4_2: FileFormat = FileFormat::new(4, 2);