Update to noodles 0.74.0

Author: zaeleus

Cargo.lock

@@ -20,7 +20,7 @@ flate2 = "1.0.14"
 git-testament = "0.2.0"
 interval-tree = { git = "https://github.com/zaeleus/interval-tree.git", rev = "e303d7254d53de5c418d6079d4b66c30c10958d4" }
 mimalloc = { version = "0.1.26", default-features = false }
-noodles = { version = "0.73.0", features = ["bam", "bgzf", "core", "gff", "sam"] }
+noodles = { version = "0.74.0", features = ["bam", "bgzf", "core", "gff", "sam"] }
 noodles-bgzf = { version = "0.30.0", features = ["libdeflate"] }
 thiserror = "1.0.40"
 tracing = "0.1.25"

Cargo.toml

@@ -70,14 +70,16 @@ pub fn read_features<R>(
 where
     R: BufRead,
 {
+    use noodles::gff::lazy::{record::attributes::field::Value, Line};
+
     let mut features: HashMap<String, Vec<Feature>> = HashMap::new();
 
     info!("reading features");
 
-    let mut line = noodles::gff::lazy::Line::default();
+    let mut line = Line::default();
 
     while reader.read_lazy_line(&mut line)? != 0 {
-        let noodles::gff::lazy::Line::Record(ref record) = line else {
+        let Line::Record(ref record) = line else {
             continue;
         };
 
@@ -86,17 +88,21 @@ where
         }
 
         let reference_sequence_name = record.reference_sequence_name();
-        let start = record.start().try_into()?;
-        let end = record.end().try_into()?;
-        let strand = record.strand().try_into()?;
+        let start = record.start()?;
+        let end = record.end()?;
+        let strand = record.strand()?;
 
         let feature = Feature::new(reference_sequence_name.into(), start, end, strand);
 
         let attributes = record.attributes();
         let id = attributes
             .get(feature_id)
             .ok_or_else(|| ReadFeaturesError::MissingAttribute(feature_id.into()))?
-            .map_err(|_| ReadFeaturesError::InvalidAttribute(feature_id.into()))?;
+            .map_err(|_| ReadFeaturesError::InvalidAttribute(feature_id.into()))
+            .and_then(|value| match value {
+                Value::String(s) => Ok(s),
+                Value::Array(_) => Err(ReadFeaturesError::InvalidAttribute(feature_id.into())),
+            })?;
 
         let list = features.entry(id.into()).or_default();