diff --git a/Cargo.toml b/Cargo.toml
index 0b44546..4d116b0 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -10,7 +10,7 @@ name = "biobear"
 [dependencies]
 arrow = { version = "52.1.0", features = ["pyarrow"] }
 datafusion = "40"
-exon = { version = "0.29.1", features = ["default"] }
+exon = { version = "0.30.0", features = ["default"] }
 pyo3 = "0.21.2"
 tokio = { version = "1", features = ["rt"] }
 noodles = { version = "0.78", features = ["core"] }
diff --git a/src/datasources/bed.rs b/src/datasources/bed.rs
index 3b1fe40..a886877 100644
--- a/src/datasources/bed.rs
+++ b/src/datasources/bed.rs
@@ -15,7 +15,7 @@
 use exon::datasources::bed::table_provider::ListingBEDTableOptions;
 use pyo3::{pyclass, pymethods};
 
-use crate::{error::BioBearResult, file_options::FileOptions, FileCompressionType};
+use crate::{file_options::impl_settable_from_file_options, FileCompressionType};
 
 #[pyclass]
 #[derive(Debug, Clone, Default)]
@@ -31,6 +31,8 @@ pub struct BEDReadOptions {
     file_extension: Option<String>,
 }
 
+impl_settable_from_file_options!(BEDReadOptions);
+
 #[pymethods]
 impl BEDReadOptions {
     #[new]
@@ -48,28 +50,6 @@ impl BEDReadOptions {
     }
 }
 
-impl BEDReadOptions {
-    pub(crate) fn update_from_file_options(
-        &mut self,
-        file_options: &FileOptions,
-    ) -> BioBearResult<()> {
-        if let Some(file_extension) = file_options.file_extension() {
-            if self.file_extension.is_none() {
-                self.file_extension = Some(file_extension.to_string());
-            }
-        }
-
-        if let Some(file_compression_type) = file_options.file_compression_type() {
-            if self.file_compression_type.is_none() {
-                let fct = FileCompressionType::try_from(file_compression_type)?;
-                self.file_compression_type = Some(fct);
-            }
-        }
-
-        Ok(())
-    }
-}
-
 impl From<BEDReadOptions> for ListingBEDTableOptions {
     fn from(options: BEDReadOptions) -> Self {
         let file_compression_type = options
diff --git a/src/datasources/fasta.rs b/src/datasources/fasta.rs
index 0bc18e9..eb3964c 100644
--- a/src/datasources/fasta.rs
+++ b/src/datasources/fasta.rs
@@ -13,7 +13,7 @@
 // limitations under the License.
 
 use crate::{
-    error::BioBearResult, file_compression_type::FileCompressionType, file_options::FileOptions,
+    file_compression_type::FileCompressionType, file_options::impl_settable_from_file_options,
 };
 use exon::datasources::fasta::{table_provider::ListingFASTATableOptions, SequenceDataType};
 use pyo3::{pyclass, pymethods};
@@ -107,27 +107,7 @@ impl FASTAReadOptions {
     }
 }
 
-impl FASTAReadOptions {
-    pub(crate) fn update_from_file_options(
-        &mut self,
-        file_options: &FileOptions,
-    ) -> BioBearResult<()> {
-        if let Some(file_extension) = file_options.file_extension() {
-            if self.file_extension.is_none() {
-                self.file_extension = Some(file_extension.to_string());
-            }
-        }
-
-        if let Some(file_compression_type) = file_options.file_compression_type() {
-            if self.file_compression_type.is_none() {
-                let fct = FileCompressionType::try_from(file_compression_type)?;
-                self.file_compression_type = Some(fct);
-            }
-        }
-
-        Ok(())
-    }
-}
+impl_settable_from_file_options!(FASTAReadOptions);
 
 impl From<FASTAReadOptions> for ListingFASTATableOptions {
     fn from(options: FASTAReadOptions) -> Self {
diff --git a/src/datasources/fastq.rs b/src/datasources/fastq.rs
index bf4292b..1401bd4 100644
--- a/src/datasources/fastq.rs
+++ b/src/datasources/fastq.rs
@@ -13,7 +13,7 @@
 // limitations under the License.
 
 use crate::{
-    error::BioBearResult, file_compression_type::FileCompressionType, file_options::FileOptions,
+    file_compression_type::FileCompressionType, file_options::impl_settable_from_file_options,
 };
 use exon::datasources::fastq::table_provider::ListingFASTQTableOptions;
 use pyo3::{pyclass, pymethods};
@@ -51,6 +51,8 @@ pub struct FASTQReadOptions {
     file_compression_type: Option<FileCompressionType>,
 }
 
+impl_settable_from_file_options!(FASTQReadOptions);
+
 #[pymethods]
 impl FASTQReadOptions {
     #[new]
@@ -84,24 +86,6 @@ impl FASTQReadOptions {
     }
 }
 
-impl FASTQReadOptions {
-    pub(crate) fn update_from_file_options(
-        &mut self,
-        file_options: &FileOptions,
-    ) -> BioBearResult<()> {
-        if let Some(file_extension) = file_options.file_extension() {
-            self.file_extension = Some(file_extension.to_string());
-        }
-
-        if let Some(file_compression_type) = file_options.file_compression_type() {
-            let fct = FileCompressionType::try_from(file_compression_type)?;
-            self.file_compression_type = Some(fct);
-        }
-
-        Ok(())
-    }
-}
-
 impl From<FASTQReadOptions> for ListingFASTQTableOptions {
     fn from(options: FASTQReadOptions) -> Self {
         let file_compression_type = options
diff --git a/src/datasources/genbank.rs b/src/datasources/genbank.rs
index 69be665..13715c9 100644
--- a/src/datasources/genbank.rs
+++ b/src/datasources/genbank.rs
@@ -15,28 +15,37 @@
 use exon::datasources::genbank::table_provider::ListingGenbankTableOptions;
 use pyo3::{pyclass, pymethods};
 
-use crate::FileCompressionType;
+use crate::{file_options::impl_settable_from_file_options, FileCompressionType};
 
 #[pyclass]
 #[derive(Debug, Clone, Default)]
 /// Options for reading GenBank files.
 pub struct GenBankReadOptions {
     /// The file compression type.
-    file_compression_type: FileCompressionType,
+    file_compression_type: Option<FileCompressionType>,
+    /// The file extension.
+    file_extension: Option<String>,
 }
 
+impl_settable_from_file_options!(GenBankReadOptions);
+
 #[pymethods]
 impl GenBankReadOptions {
     #[new]
     fn new(file_compression_type: Option<FileCompressionType>) -> Self {
         Self {
-            file_compression_type: file_compression_type.unwrap_or_default(),
+            file_compression_type,
+            file_extension: Some("gb".to_string()),
         }
     }
 }
 
 impl From<GenBankReadOptions> for ListingGenbankTableOptions {
     fn from(options: GenBankReadOptions) -> Self {
-        ListingGenbankTableOptions::new(options.file_compression_type.into())
+        let c = options
+            .file_compression_type
+            .unwrap_or(FileCompressionType::UNCOMPRESSED);
+
+        ListingGenbankTableOptions::new(c.into())
     }
 }
diff --git a/src/datasources/gff.rs b/src/datasources/gff.rs
index df5de45..4dcbea5 100644
--- a/src/datasources/gff.rs
+++ b/src/datasources/gff.rs
@@ -16,7 +16,11 @@ use exon::datasources::gff::table_provider::ListingGFFTableOptions;
 use noodles::core::Region;
 use pyo3::{pyclass, pymethods, PyResult};
 
-use crate::{error::BioBearResult, file_options::FileOptions, FileCompressionType};
+use crate::{
+    error::BioBearResult,
+    file_options::{impl_settable_from_file_options, FileOptions},
+    FileCompressionType,
+};
 
 use super::parse_region;
 
@@ -28,6 +32,8 @@ pub struct GFFReadOptions {
     file_compression_type: Option<FileCompressionType>,
 }
 
+impl_settable_from_file_options!(GFFReadOptions);
+
 #[pymethods]
 impl GFFReadOptions {
     #[new]
@@ -56,8 +62,7 @@ impl GFFReadOptions {
 
         if let Some(file_compression_type) = options.file_compression_type() {
             if self.file_compression_type.is_none() {
-                let fct = FileCompressionType::try_from(file_compression_type)?;
-                self.file_compression_type = Some(fct);
+                self.file_compression_type = Some(file_compression_type);
             }
         }
 
diff --git a/src/datasources/gtf.rs b/src/datasources/gtf.rs
index 778adbd..44cd83a 100644
--- a/src/datasources/gtf.rs
+++ b/src/datasources/gtf.rs
@@ -15,35 +15,44 @@
 use exon::datasources::gtf::table_provider::ListingGTFTableOptions;
 use pyo3::{pyclass, pymethods};
 
-use crate::FileCompressionType;
+use crate::{file_options::impl_settable_from_file_options, FileCompressionType};
 
 #[pyclass]
 #[derive(Debug, Clone)]
 pub struct GTFReadOptions {
-    file_compression_type: FileCompressionType,
+    file_compression_type: Option<FileCompressionType>,
+    file_extension: Option<String>,
 }
 
 impl Default for GTFReadOptions {
     fn default() -> Self {
         Self {
-            file_compression_type: FileCompressionType::UNCOMPRESSED,
+            file_compression_type: Some(FileCompressionType::UNCOMPRESSED),
+            file_extension: None,
         }
     }
 }
 
+impl_settable_from_file_options!(GTFReadOptions);
+
 #[pymethods]
 impl GTFReadOptions {
     #[new]
     pub fn new(file_compression_type: Option<FileCompressionType>) -> Self {
         Self {
-            file_compression_type: file_compression_type
-                .unwrap_or(FileCompressionType::UNCOMPRESSED),
+            file_compression_type,
+            file_extension: Some("gtf".to_string()),
         }
     }
 }
 
 impl From<GTFReadOptions> for ListingGTFTableOptions {
     fn from(options: GTFReadOptions) -> Self {
-        ListingGTFTableOptions::new(options.file_compression_type.into())
+        ListingGTFTableOptions::new(
+            options
+                .file_compression_type
+                .map(|c| c.into())
+                .unwrap_or(datafusion::datasource::file_format::file_compression_type::FileCompressionType::UNCOMPRESSED),
+        )
     }
 }
diff --git a/src/datasources/mzml.rs b/src/datasources/mzml.rs
index dac65e7..4ebb742 100644
--- a/src/datasources/mzml.rs
+++ b/src/datasources/mzml.rs
@@ -15,19 +15,23 @@
 use exon::datasources::mzml::table_provider::ListingMzMLTableOptions;
 use pyo3::{pyclass, pymethods};
 
-use crate::FileCompressionType;
+use crate::{file_options::impl_settable_from_file_options, FileCompressionType};
 
 #[pyclass]
 #[derive(Debug, Clone)]
 /// Options for reading mzML files.
 pub struct MzMLReadOptions {
-    file_compression_type: FileCompressionType,
+    file_compression_type: Option<FileCompressionType>,
+    file_extension: Option<String>,
 }
 
+impl_settable_from_file_options!(MzMLReadOptions);
+
 impl Default for MzMLReadOptions {
     fn default() -> Self {
         Self {
-            file_compression_type: FileCompressionType::UNCOMPRESSED,
+            file_compression_type: Some(FileCompressionType::UNCOMPRESSED),
+            file_extension: None,
         }
     }
 }
@@ -37,14 +41,28 @@ impl MzMLReadOptions {
     #[new]
     fn new(file_compression_type: Option<FileCompressionType>) -> Self {
         Self {
-            file_compression_type: file_compression_type
-                .unwrap_or(FileCompressionType::UNCOMPRESSED),
+            file_compression_type: Some(
+                file_compression_type.unwrap_or(FileCompressionType::UNCOMPRESSED),
+            ),
+            file_extension: None,
         }
     }
 }
 
 impl From<MzMLReadOptions> for ListingMzMLTableOptions {
     fn from(options: MzMLReadOptions) -> Self {
-        ListingMzMLTableOptions::new(options.file_compression_type.into())
+        let file_compression_type = options
+            .file_compression_type
+            .unwrap_or(FileCompressionType::UNCOMPRESSED);
+
+        let mut new_options = ListingMzMLTableOptions::new(file_compression_type.into());
+
+        // let file_extension = options.file_extension;
+        if let Some(fe) = options.file_extension {
+            eprintln!("Setting file extension to {}", fe);
+            new_options = new_options.with_file_extension(fe)
+        }
+
+        new_options
     }
 }
diff --git a/src/datasources/vcf.rs b/src/datasources/vcf.rs
index 06c8b70..9f7dfe2 100644
--- a/src/datasources/vcf.rs
+++ b/src/datasources/vcf.rs
@@ -17,7 +17,7 @@ use exon::datasources::vcf::ListingVCFTableOptions;
 use noodles::core::Region;
 use pyo3::{pyclass, pymethods, PyResult};
 
-use crate::FileCompressionType;
+use crate::{file_options::impl_settable_from_file_options, FileCompressionType};
 
 use super::parse_region;
 
@@ -28,15 +28,19 @@ pub struct VCFReadOptions {
     /// The region to read.
     region: Option<Region>,
     /// The file compression type.
-    file_compression_type: FileCompressionType,
+    file_compression_type: Option<FileCompressionType>,
     /// True if the INFO column should be parsed.
     parse_info: bool,
     /// True if the FORMAT column should be parsed.
     parse_formats: bool,
     /// The partition fields.
     partition_cols: Option<Vec<String>>,
+    /// The file extension.
+    file_extension: Option<String>,
 }
 
+impl_settable_from_file_options!(VCFReadOptions);
+
 #[pymethods]
 impl VCFReadOptions {
     #[new]
@@ -50,22 +54,24 @@ impl VCFReadOptions {
     ) -> PyResult<Self> {
         let region = parse_region(region)?;
 
-        let file_compression_type =
-            file_compression_type.unwrap_or(FileCompressionType::UNCOMPRESSED);
-
         Ok(Self {
             region,
             file_compression_type,
             parse_info,
             parse_formats,
             partition_cols,
+            file_extension: Some("vcf".to_string()),
         })
     }
 }
 
 impl From<VCFReadOptions> for ListingVCFTableOptions {
     fn from(options: VCFReadOptions) -> Self {
-        let mut o = ListingVCFTableOptions::new(options.file_compression_type.into(), false)
+        let compression = options
+            .file_compression_type
+            .unwrap_or(FileCompressionType::UNCOMPRESSED);
+
+        let mut o = ListingVCFTableOptions::new(compression.into(), false)
             .with_parse_info(options.parse_info)
             .with_parse_formats(options.parse_formats);
 
diff --git a/src/file_compression_type.rs b/src/file_compression_type.rs
index 0012fef..a0f43c2 100644
--- a/src/file_compression_type.rs
+++ b/src/file_compression_type.rs
@@ -23,7 +23,7 @@ use pyo3::prelude::*;
 use crate::error::BioBearError;
 
 #[pyclass]
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, PartialEq)]
 pub enum FileCompressionType {
     GZIP,
     ZSTD,
diff --git a/src/file_options.rs b/src/file_options.rs
index c367a04..ef83d52 100644
--- a/src/file_options.rs
+++ b/src/file_options.rs
@@ -12,19 +12,20 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-use std::{path::Path, str::FromStr};
-
-use datafusion::datasource::file_format::file_compression_type::FileCompressionType;
+use std::path::Path;
+use std::str::FromStr;
 
 use crate::error::BioBearResult;
+use crate::FileCompressionType;
 
 mod settable_from_file_options;
+pub(crate) use settable_from_file_options::impl_settable_from_file_options;
 pub(crate) use settable_from_file_options::SettableFromFileOptions;
 
 #[derive(Debug, Clone, Default)]
 pub(crate) struct FileOptions {
     file_extension: Option<String>,
-    file_compression_type: Option<FileCompressionType>,
+    file_compression_type: Option<crate::FileCompressionType>,
 }
 
 impl FileOptions {
@@ -32,22 +33,22 @@ impl FileOptions {
         self.file_extension.as_deref()
     }
 
-    pub fn file_compression_type(&self) -> Option<FileCompressionType> {
-        self.file_compression_type
+    pub fn file_compression_type(&self) -> Option<crate::FileCompressionType> {
+        self.file_compression_type.clone()
     }
 
     pub fn set_from_file_options(
-        &mut self,
+        &self,
         settable: &mut dyn settable_from_file_options::SettableFromFileOptions,
     ) -> BioBearResult<()> {
-        if let Some(file_extension) = self.file_extension() {
-            let file_options = settable.file_extension_mut();
-            *file_options = Some(file_extension.to_string());
+        if settable.file_extension_mut().is_none() {
+            let file_extension_option = settable.file_extension_mut();
+            *file_extension_option = self.file_extension().map(|ext| ext.to_string());
         }
 
         if let Some(file_compression_type) = self.file_compression_type() {
             let file_options = settable.file_compression_type_mut();
-            *file_options = Some(crate::FileCompressionType::try_from(file_compression_type)?);
+            *file_options = Some(file_compression_type.clone());
         }
 
         Ok(())
@@ -86,6 +87,8 @@ impl From<&str> for FileOptions {
 
 #[cfg(test)]
 mod tests {
+    use crate::FileCompressionType;
+
     use super::*;
 
     #[test]
diff --git a/src/file_options/settable_from_file_options.rs b/src/file_options/settable_from_file_options.rs
index e057eb7..9f2ae84 100644
--- a/src/file_options/settable_from_file_options.rs
+++ b/src/file_options/settable_from_file_options.rs
@@ -19,3 +19,19 @@ pub(crate) trait SettableFromFileOptions {
 
     fn file_compression_type_mut(&mut self) -> &mut Option<FileCompressionType>;
 }
+
+macro_rules! impl_settable_from_file_options {
+    ($struct_name:ident) => {
+        impl crate::file_options::SettableFromFileOptions for $struct_name {
+            fn file_extension_mut(&mut self) -> &mut Option<String> {
+                &mut self.file_extension
+            }
+
+            fn file_compression_type_mut(&mut self) -> &mut Option<FileCompressionType> {
+                &mut self.file_compression_type
+            }
+        }
+    };
+}
+
+pub(crate) use impl_settable_from_file_options;
diff --git a/src/session_context.rs b/src/session_context.rs
index a8288ae..443cb7a 100644
--- a/src/session_context.rs
+++ b/src/session_context.rs
@@ -56,7 +56,10 @@ impl BioBearSessionContext {
         options: Option<crate::datasources::vcf::VCFReadOptions>,
         py: Python,
     ) -> PyResult<ExecutionResult> {
-        let options = options.unwrap_or_default();
+        let file_options = FileOptions::from(file_path);
+        let mut options = options.unwrap_or_default();
+
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_vcf(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;
@@ -71,7 +74,10 @@ impl BioBearSessionContext {
         options: Option<HMMDomTabReadOptions>,
         py: Python,
     ) -> PyResult<ExecutionResult> {
-        let options = options.unwrap_or_default();
+        let file_options = FileOptions::from(file_path);
+        let mut options = options.unwrap_or_default();
+
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_hmm_dom_tab(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;
@@ -86,7 +92,7 @@ impl BioBearSessionContext {
         options: Option<crate::datasources::sdf::SDFReadOptions>,
         py: Python,
     ) -> PyResult<ExecutionResult> {
-        let mut file_options = FileOptions::from(file_path);
+        let file_options = FileOptions::from(file_path);
         let mut options = options.unwrap_or_default();
 
         file_options.set_from_file_options(&mut options)?;
@@ -151,7 +157,8 @@ impl BioBearSessionContext {
     ) -> PyResult<ExecutionResult> {
         let file_options = FileOptions::from(file_path);
         let mut options = options.unwrap_or_default();
-        options.update_from_file_options(&file_options)?;
+
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_fastq(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;
@@ -166,7 +173,10 @@ impl BioBearSessionContext {
         options: Option<crate::datasources::genbank::GenBankReadOptions>,
         py: Python,
     ) -> PyResult<ExecutionResult> {
-        let options = options.unwrap_or_default();
+        let file_options = FileOptions::from(file_path);
+        let mut options = options.unwrap_or_default();
+
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_genbank(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;
@@ -196,7 +206,10 @@ impl BioBearSessionContext {
         options: Option<MzMLReadOptions>,
         py: Python,
     ) -> PyResult<ExecutionResult> {
-        let options = options.unwrap_or_default();
+        let file_options = FileOptions::from(file_path);
+        let mut options = options.unwrap_or_default();
+
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_mzml(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;
@@ -211,7 +224,10 @@ impl BioBearSessionContext {
         options: Option<crate::datasources::gtf::GTFReadOptions>,
         py: Python,
     ) -> PyResult<ExecutionResult> {
-        let options = options.unwrap_or_default();
+        let file_options = FileOptions::from(file_path);
+        let mut options = options.unwrap_or_default();
+
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_gtf(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;
@@ -242,8 +258,9 @@ impl BioBearSessionContext {
         py: Python,
     ) -> PyResult<ExecutionResult> {
         let file_options = FileOptions::from(file_path);
+
         let mut options = options.unwrap_or_default();
-        options.update_from_file_options(&file_options)?;
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_fasta(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;
@@ -260,7 +277,8 @@ impl BioBearSessionContext {
     ) -> PyResult<ExecutionResult> {
         let file_options = FileOptions::from(file_path);
         let mut options = options.unwrap_or_default();
-        options.update_from_file_options(&file_options)?;
+
+        file_options.set_from_file_options(&mut options)?;
 
         let result = self.ctx.read_bed(file_path, options.into());
         let df = wait_for_future(py, result).map_err(error::BioBearError::from)?;