vcf/header/parser: Keep existing record in header on a duplicate ID e…

…rror
zaeleus · Dec 20, 2024 · 4b6ee3d · 4b6ee3d
1 parent a14bb31
commit 4b6ee3d
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Showing 9 changed files with 34 additions and 66 deletions.
diff --git a/noodles-vcf/CHANGELOG.md b/noodles-vcf/CHANGELOG.md
@@ -8,6 +8,10 @@
 
     This can be used to read the raw VCF header.
 
+### Changed
+
+  * vcf/header/parser: Keep existing record in header on a duplicate ID error.
+
 ## 0.69.0 - 2024-12-12
 
 ### Changed

diff --git a/noodles-vcf/src/header/parser.rs b/noodles-vcf/src/header/parser.rs
@@ -236,10 +236,7 @@ fn try_insert_info(
                 .map(|(k, v)| self::Entry::Info(k, v))
                 .unwrap())
         }
-        Entry::Occupied(entry) => {
-            let (id, _) = entry.swap_remove_entry();
-            Err(ParseError::DuplicateInfoId(id))
-        }
+        Entry::Occupied(entry) => Err(ParseError::DuplicateInfoId(entry.key().into())),
     }
 }
 
@@ -262,10 +259,7 @@ fn try_insert_filter(
                 .map(|(k, v)| self::Entry::Filter(k, v))
                 .unwrap())
         }
-        Entry::Occupied(entry) => {
-            let (id, _) = entry.swap_remove_entry();
-            Err(ParseError::DuplicateFilterId(id))
-        }
+        Entry::Occupied(entry) => Err(ParseError::DuplicateFilterId(entry.key().into())),
     }
 }
 
@@ -288,10 +282,7 @@ fn try_insert_format(
                 .map(|(k, v)| self::Entry::Format(k, v))
                 .unwrap())
         }
-        Entry::Occupied(entry) => {
-            let (id, _) = entry.swap_remove_entry();
-            Err(ParseError::DuplicateFormatId(id))
-        }
+        Entry::Occupied(entry) => Err(ParseError::DuplicateFormatId(entry.key().into())),
     }
 }
 
@@ -314,10 +305,7 @@ fn try_insert_alternative_allele(
                 .map(|(k, v)| self::Entry::AlternativeAllele(k, v))
                 .unwrap())
         }
-        Entry::Occupied(entry) => {
-            let (id, _) = entry.swap_remove_entry();
-            Err(ParseError::DuplicateAlternativeAlleleId(id))
-        }
+        Entry::Occupied(entry) => Err(ParseError::DuplicateAlternativeAlleleId(entry.key().into())),
     }
 }
 
@@ -340,10 +328,7 @@ fn try_insert_contig(
                 .map(|(k, v)| self::Entry::Contig(k, v))
                 .unwrap())
         }
-        Entry::Occupied(entry) => {
-            let (id, _) = entry.swap_remove_entry();
-            Err(ParseError::DuplicateContigId(id))
-        }
+        Entry::Occupied(entry) => Err(ParseError::DuplicateContigId(entry.key().into())),
     }
 }
 

diff --git a/noodles-vcf/src/header/parser/record/value/map/alternative_allele.rs b/noodles-vcf/src/header/parser/record/value/map/alternative_allele.rs
@@ -123,13 +123,10 @@ fn try_insert(
             entry.insert(value);
             Ok(())
         }
-        Entry::Occupied(entry) => {
-            let (t, _) = entry.swap_remove_entry();
-            Err(ParseError::new(
-                id.clone(),
-                ParseErrorKind::DuplicateTag(Tag::Other(t)),
-            ))
-        }
+        Entry::Occupied(entry) => Err(ParseError::new(
+            id.clone(),
+            ParseErrorKind::DuplicateTag(Tag::Other(entry.key().clone())),
+        )),
     }
 }
 

diff --git a/noodles-vcf/src/header/parser/record/value/map/contig.rs b/noodles-vcf/src/header/parser/record/value/map/contig.rs
@@ -146,13 +146,10 @@ fn try_insert(
             entry.insert(value);
             Ok(())
         }
-        Entry::Occupied(entry) => {
-            let (t, _) = entry.swap_remove_entry();
-            Err(ParseError::new(
-                id.clone(),
-                ParseErrorKind::DuplicateTag(Tag::Other(t)),
-            ))
-        }
+        Entry::Occupied(entry) => Err(ParseError::new(
+            id.clone(),
+            ParseErrorKind::DuplicateTag(Tag::Other(entry.key().clone())),
+        )),
     }
 }
 

diff --git a/noodles-vcf/src/header/parser/record/value/map/filter.rs b/noodles-vcf/src/header/parser/record/value/map/filter.rs
@@ -134,13 +134,10 @@ fn try_insert(
             entry.insert(value);
             Ok(())
         }
-        Entry::Occupied(entry) => {
-            let (t, _) = entry.swap_remove_entry();
-            Err(ParseError::new(
-                id.clone(),
-                ParseErrorKind::DuplicateTag(Tag::Other(t)),
-            ))
-        }
+        Entry::Occupied(entry) => Err(ParseError::new(
+            id.clone(),
+            ParseErrorKind::DuplicateTag(Tag::Other(entry.key().clone())),
+        )),
     }
 }
 

diff --git a/noodles-vcf/src/header/parser/record/value/map/format.rs b/noodles-vcf/src/header/parser/record/value/map/format.rs
@@ -178,13 +178,10 @@ fn try_insert(
             entry.insert(value);
             Ok(())
         }
-        Entry::Occupied(entry) => {
-            let (t, _) = entry.swap_remove_entry();
-            Err(ParseError::new(
-                id.clone(),
-                ParseErrorKind::DuplicateTag(Tag::Other(t)),
-            ))
-        }
+        Entry::Occupied(entry) => Err(ParseError::new(
+            id.clone(),
+            ParseErrorKind::DuplicateTag(Tag::Other(entry.key().clone())),
+        )),
     }
 }
 

diff --git a/noodles-vcf/src/header/parser/record/value/map/info.rs b/noodles-vcf/src/header/parser/record/value/map/info.rs
@@ -178,13 +178,10 @@ fn try_insert(
             entry.insert(value);
             Ok(())
         }
-        Entry::Occupied(entry) => {
-            let (t, _) = entry.swap_remove_entry();
-            Err(ParseError::new(
-                id.clone(),
-                ParseErrorKind::DuplicateTag(Tag::Other(t)),
-            ))
-        }
+        Entry::Occupied(entry) => Err(ParseError::new(
+            id.clone(),
+            ParseErrorKind::DuplicateTag(Tag::Other(entry.key().clone())),
+        )),
     }
 }
 

diff --git a/noodles-vcf/src/header/parser/record/value/map/other.rs b/noodles-vcf/src/header/parser/record/value/map/other.rs
@@ -283,13 +283,10 @@ fn try_insert(
             entry.insert(value);
             Ok(())
         }
-        Entry::Occupied(entry) => {
-            let (t, _) = entry.swap_remove_entry();
-            Err(ParseError::new(
-                id.clone(),
-                ParseErrorKind::DuplicateTag(Tag::Other(t)),
-            ))
-        }
+        Entry::Occupied(entry) => Err(ParseError::new(
+            id.clone(),
+            ParseErrorKind::DuplicateTag(Tag::Other(entry.key().clone())),
+        )),
     }
 }
 

diff --git a/noodles-vcf/src/header/record/value/collection.rs b/noodles-vcf/src/header/record/value/collection.rs
@@ -61,10 +61,7 @@ fn try_insert(
             entry.insert(m);
             Ok(())
         }
-        Entry::Occupied(entry) => {
-            let (id, _) = entry.swap_remove_entry();
-            Err(AddError::DuplicateId(id))
-        }
+        Entry::Occupied(entry) => Err(AddError::DuplicateId(entry.key().into())),
     }
 }