feat: add bed

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

@@ -24,3 +24,6 @@ pub mod table_provider;
 
 pub use self::file_opener::BEDOpener;
 pub use self::scanner::BEDScan;
+
+mod udtf;
+pub use self::udtf::BEDScanFunction;

exon/exon-core/src/datasources/bed/udtf.rs

@@ -0,0 +1,48 @@
+// Copyright 2023 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::sync::Arc;
+
+use crate::datasources::ScanFunction;
+use datafusion::{
+    datasource::{function::TableFunctionImpl, TableProvider},
+    error::Result,
+    logical_expr::Expr,
+};
+use exon_bed::BEDSchemaBuilder;
+
+use super::table_provider::{ListingBEDTable, ListingBEDTableConfig, ListingBEDTableOptions};
+
+/// A table function that returns a table provider for a BED file.
+#[derive(Debug, Default)]
+pub struct BEDScanFunction {}
+
+impl TableFunctionImpl for BEDScanFunction {
+    fn call(&self, exprs: &[Expr]) -> Result<Arc<dyn TableProvider>> {
+        let listing_scan_function = ScanFunction::try_from(exprs)?;
+
+        let schema = BEDSchemaBuilder::default().build();
+
+        let listing_table_options =
+            ListingBEDTableOptions::new(listing_scan_function.file_compression_type);
+
+        let listing_fasta_table_config =
+            ListingBEDTableConfig::new(listing_scan_function.listing_table_url)
+                .with_options(listing_table_options);
+
+        let listing_fasta_table = ListingBEDTable::try_new(listing_fasta_table_config, schema)?;
+
+        Ok(Arc::new(listing_fasta_table))
+    }
+}

exon/exon-core/src/session_context/exon_context_ext.rs

@@ -29,6 +29,7 @@ use noodles::core::Region;
 use crate::{
     datasources::{
         bcf::table_provider::{ListingBCFTable, ListingBCFTableConfig, ListingBCFTableOptions},
+        bed::BEDScanFunction,
         fasta::FastaScanFunction,
         fastq::FastqScanFunction,
         gff::GFFScanFunction,
@@ -160,6 +161,7 @@ pub trait ExonSessionExt {
         ctx.register_udtf("fastq_scan", Arc::new(FastqScanFunction::default()));
         ctx.register_udtf("gff_scan", Arc::new(GFFScanFunction::default()));
         ctx.register_udtf("gtf_scan", Arc::new(GTFScanFunction::default()));
+        ctx.register_udtf("bed_scan", Arc::new(BEDScanFunction::default()));
 
         ctx
     }

exon/exon-core/tests/sqllogictests/slt/bed-select-tests.slt

@@ -26,3 +26,18 @@ chr1 11874 12227 NR_046018_exon_0_0_chr1_11874_f NULL + NULL NULL NULL NULL NULL
 
 statement ok
 DROP TABLE bed;
+
+query T
+SELECT COUNT(*) FROM bed_scan('$CARGO_MANIFEST_DIR/test-data/datasources/bed/test.bed');
+----
+10
+
+query T
+SELECT COUNT(*) FROM bed_scan('$CARGO_MANIFEST_DIR/test-data/datasources/bed-partition/');
+----
+20
+
+query T
+SELECT COUNT(*) FROM bed_scan('$CARGO_MANIFEST_DIR/test-data/datasources/bed/test.bed.gz', 'gzip');
+----
+1