feat: update noodles (#596)

Cargo.toml

@@ -39,7 +39,7 @@ arrow = { version = "52.2.0" }
 async-trait = "0.1.81"
 datafusion = { version = "40", features = ["compression", "parquet"] }
 futures = "0.3"
-noodles = { version = "0.78" }
+noodles = { version = "0.79" }
 object_store = { version = "0.10.2" }
 tokio = { version = "1", features = ["io-util"] }
 tokio-util = { version = "0.7.11", features = ["compat"] }

exon/exon-bam/src/array_builder.rs

@@ -21,7 +21,7 @@ use arrow::{
 use exon_common::ExonArrayBuilder;
 use exon_sam::TagsBuilder;
 use noodles::sam::{
-    alignment::record::{cigar::op::Kind, Cigar, Name},
+    alignment::record::{cigar::op::Kind, Cigar},
     Header,
 };
 
@@ -104,7 +104,7 @@ impl BAMArrayBuilder {
             match col_idx {
                 0 => {
                     if let Some(name) = record.record().name() {
-                        let sam_read_name = std::str::from_utf8(name.as_bytes())?;
+                        let sam_read_name = std::str::from_utf8(name)?;
 
                         self.names.append_value(sam_read_name);
                     } else {

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

@@ -162,17 +162,6 @@ impl ListingCRAMTableOptions {
         let stream_reader = Box::pin(get_result.into_stream().map_err(ExonError::from));
         let stream_reader = StreamReader::new(stream_reader);
 
-        let mut cram_reader = noodles::cram::AsyncReader::new(stream_reader);
-
-        cram_reader.read_file_definition().await?;
-        let header = cram_reader.read_file_header().await?;
-        let header: Header = header
-            .to_owned()
-            .parse()
-            .map_err(|_| DataFusionError::Execution("Unable to parse header".to_string()))?;
-
-        let mut schema_builder = SAMSchemaBuilder::default();
-
         let reference_sequence_repository = match &self.fasta_reference {
             Some(reference) => {
                 let object_store_adapter = ObjectStoreFastaRepositoryAdapter::try_new(
@@ -186,11 +175,20 @@ impl ListingCRAMTableOptions {
             None => noodles::fasta::Repository::default(),
         };
 
-        if let Some(Ok(record)) = cram_reader
-            .records(&reference_sequence_repository, &header)
-            .next()
-            .await
-        {
+        let mut cram_reader = noodles::cram::r#async::io::reader::Builder::default()
+            .set_reference_sequence_repository(reference_sequence_repository)
+            .build_from_reader(stream_reader);
+
+        cram_reader.read_file_definition().await?;
+        let header = cram_reader.read_file_header().await?;
+        let header: Header = header
+            .to_owned()
+            .parse()
+            .map_err(|_| DataFusionError::Execution("Unable to parse header".to_string()))?;
+
+        let mut schema_builder = SAMSchemaBuilder::default();
+
+        if let Some(Ok(record)) = cram_reader.records(&header).next().await {
             schema_builder = schema_builder.with_tags_data_type_from_data(record.data())?;
         } else {
             return Err(ExonError::ExecutionError(

exon/exon-cram/src/array_builder.rs

@@ -22,7 +22,7 @@ use exon_common::ExonArrayBuilder;
 use exon_sam::TagsBuilder;
 use noodles::{
     cram::Record as CramRecord,
-    sam::alignment::record::{cigar::op::Kind, Cigar, Name},
+    sam::alignment::record::{cigar::op::Kind, Cigar},
 };
 
 use crate::CRAMConfig;
@@ -80,8 +80,7 @@ impl CRAMArrayBuilder {
             match col_idx {
                 0 => {
                     if let Some(name) = record.name() {
-                        let sam_read_name = name.as_bytes();
-                        self.names.append_value(std::str::from_utf8(sam_read_name)?);
+                        self.names.append_value(std::str::from_utf8(name)?);
                     } else {
                         self.names.append_null();
                     }