fix: fix overflow in position conversion error

exon/exon-bam/src/error.rs

@@ -0,0 +1,40 @@
+// Copyright 2024 WHERE TRUE Technologies.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+use std::error::Error;
+
+use arrow::error::ArrowError;
+
+#[derive(Debug)]
+pub enum ExonBAMError {
+    PositionConversionError(String),
+}
+
+impl Error for ExonBAMError {}
+
+impl std::fmt::Display for ExonBAMError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            ExonBAMError::PositionConversionError(e) => {
+                write!(f, "Error converting position: {}", e)
+            }
+        }
+    }
+}
+
+impl From<ExonBAMError> for ArrowError {
+    fn from(e: ExonBAMError) -> Self {
+        ArrowError::ExternalError(Box::new(e))
+    }
+}

exon/exon-bam/src/indexed_async_batch_stream.rs

@@ -26,6 +26,8 @@ use noodles::{
 };
 use tokio::io::AsyncBufRead;
 
+use crate::ExonBAMError;
+
 use super::{array_builder::BAMArrayBuilder, BAMConfig};
 
 /// This is a semi-lazy record that can be used to filter on the region without
@@ -36,16 +38,10 @@ pub(crate) struct SemiLazyRecord {
 }
 
 impl TryFrom<RecordBuf> for SemiLazyRecord {
-    type Error = arrow::error::ArrowError;
+    type Error = ExonBAMError;
 
     fn try_from(record: RecordBuf) -> Result<Self, Self::Error> {
-        let start = record.alignment_start();
-
-        let alignment_end = start.map(|s| usize::from(s) + record.cigar().alignment_span() - 1);
-        let alignment_end = alignment_end
-            .map(Position::try_from)
-            .transpose()
-            .map_err(|e| ArrowError::ExternalError(Box::new(e)))?;
+        let alignment_end = record.alignment_end();
 
         Ok(Self {
             inner: record,

exon/exon-bam/src/lib.rs

@@ -15,9 +15,11 @@
 mod array_builder;
 mod batch_reader;
 mod config;
+mod error;
 mod indexed_async_batch_stream;
 
 pub use array_builder::BAMArrayBuilder;
 pub use batch_reader::BatchReader;
 pub use config::BAMConfig;
+pub use error::ExonBAMError;
 pub use indexed_async_batch_stream::IndexedAsyncBatchStream;