fix: update noodles

Cargo.toml

@@ -38,7 +38,7 @@ arrow = { version = "51.0.0" }
 async-trait = "0.1.80"
 datafusion = { version = "37", features = ["compression", "parquet"] }
 futures = "0.3"
-noodles = { version = "0.68" }
+noodles = { version = "0.69" }
 object_store = { version = "0.9" }
 tokio = { version = "1", features = ["io-util"] }
 tokio-util = { version = "0.7.10", features = ["compat"] }

exon/exon-bcf/src/batch_reader.rs

@@ -32,10 +32,8 @@ where
     /// Configuration for how to batch records.
     config: Arc<BCFConfig>,
 
-    /// The VCF header.
+    /// The header.
     header: Arc<noodles::vcf::Header>,
-    // The VCF header string maps.
-    // string_maps: noodles::bcf::header::StringMaps,
 }
 
 impl<R> BatchReader<R>
@@ -47,22 +45,6 @@ where
         // reader.read_file_format().await?;
 
         let header = reader.read_header().await?;
-        // let header = header_str.parse::<noodles::vcf::Header>().map_err(|e| {
-        //     std::io::Error::new(
-        //         std::io::ErrorKind::InvalidData,
-        //         format!("invalid header: {e}"),
-        //     )
-        // })?;
-
-        // let string_maps = match header_str.parse() {
-        //     Ok(string_maps) => string_maps,
-        //     Err(e) => {
-        //         return Err(std::io::Error::new(
-        //             std::io::ErrorKind::InvalidData,
-        //             format!("invalid header: {e}"),
-        //         ))
-        //     }
-        // };
 
         Ok(Self {
             reader,

exon/exon-core/src/datasources/bigwig/mod.rs

@@ -12,5 +12,8 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-pub(crate) mod value;
-pub(crate) mod zoom;
+/// Module to work with BigWig files.
+pub mod value;
+
+/// Module to work with BigWig files with a zoom level.
+pub mod zoom;

exon/exon-core/src/datasources/vcf/table_provider.rs

@@ -153,6 +153,14 @@ impl ListingVCFTableOptions {
         }
     }
 
+    /// Set the file extension
+    pub fn with_file_extension(self, file_extension: String) -> Self {
+        Self {
+            file_extension,
+            ..self
+        }
+    }
+
     /// Set the table partition columns
     pub fn with_table_partition_cols(self, table_partition_cols: Vec<Field>) -> Self {
         Self {