refactor: move out bed

Cargo.toml

@@ -12,6 +12,7 @@ members = [
   "exon-cli",
   "exon-examples",
   "exon/exon-bam",
+  "exon/exon-bed",
   "exon/exon-common",
   "exon/exon-core",
   "exon/exon-exome",

docs/release-guide.md

@@ -7,10 +7,12 @@ flowchart TD
     exon-sam --> exon-bam
     exon-sam --> exon-core
     exon-bam --> exon-core
+    exon-bed --> exon-core
     exon-common --> exon-core
     exon-fasta --> exon-core
     exon-fastq --> exon-core
     exon-gff --> exon-core
+    exon-gtf --> exon-core
     exon-io --> exon-core
     exon-core --> exon-exome
     exon-test --dev-dep--> exon-fasta
@@ -43,10 +45,12 @@ Then publish the crates:
 ```console
 # Crates that do not depend on other crates
 cargo publish --manifest-path exon/exon-bam/Cargo.toml
+cargo publish --manifest-path exon/exon-bed/Cargo.toml
 cargo publish --manifest-path exon/exon-common/Cargo.toml
 cargo publish --manifest-path exon/exon-fasta/Cargo.toml
 cargo publish --manifest-path exon/exon-fastq/Cargo.toml
 cargo publish --manifest-path exon/exon-gff/Cargo.toml
+cargo publish --manifest-path exon/exon-gtf/Cargo.toml
 cargo publish --manifest-path exon/exon-io/Cargo.toml
 
 # Crates that depend on other crates

exon/exon-bed/Cargo.toml

@@ -0,0 +1,20 @@
+[package]
+description = "Subcrate of the `exon` crate for working with BED files."
+edition.workspace = true
+homepage.workspace = true
+license.workspace = true
+name = "exon-bed"
+readme.workspace = true
+repository.workspace = true
+version.workspace = true
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+arrow = {workspace = true}
+exon-common = {path = "../exon-common", version = "0.3.9"}
+futures = {workspace = true}
+noodles = {version = "0.59", features = ["bed"]}
+object_store = {workspace = true}
+tokio = {workspace = true}
+tokio-util = {workspace = true}

exon/exon-core/src/datasources/bed/array_builder.rs → exon/exon-bed/src/array_builder.rs

@@ -15,14 +15,14 @@
 use std::sync::Arc;
 
 use arrow::{
-    array::{ArrayBuilder, ArrayRef, GenericStringBuilder, Int64Builder},
+    array::{ArrayRef, GenericStringBuilder, Int64Builder},
     datatypes::{DataType, Field, Schema},
 };
 use exon_common::TableSchema;
 
 use super::bed_record_builder::BEDRecord;
 
-pub(crate) struct BEDSchemaBuilder {
+pub struct BEDSchemaBuilder {
     file_fields: Vec<Field>,
     partition_fields: Vec<Field>,
 }
@@ -86,6 +86,8 @@ pub struct BEDArrayBuilder {
     block_counts: Int64Builder,
     block_sizes: GenericStringBuilder<i32>,
     block_starts: GenericStringBuilder<i32>,
+
+    rows: usize,
 }
 
 impl BEDArrayBuilder {
@@ -103,11 +105,16 @@ impl BEDArrayBuilder {
             block_counts: Int64Builder::new(),
             block_sizes: GenericStringBuilder::<i32>::new(),
             block_starts: GenericStringBuilder::<i32>::new(),
+            rows: 0,
         }
     }
 
     pub fn len(&self) -> usize {
-        self.reference_sequence_names.len()
+        self.rows
+    }
+
+    pub fn is_empty(&self) -> bool {
+        self.rows == 0
     }
 
     pub fn append(&mut self, record: BEDRecord) -> std::io::Result<()> {
@@ -133,6 +140,8 @@ impl BEDArrayBuilder {
         self.block_sizes.append_option(record.block_sizes);
         self.block_starts.append_option(record.block_starts);
 
+        self.rows += 1;
+
         Ok(())
     }
 

exon/exon-core/src/datasources/bed/batch_reader.rs → exon/exon-bed/src/batch_reader.rs

@@ -67,7 +67,7 @@ where
             }
         }
 
-        if array_builder.len() == 0 {
+        if array_builder.is_empty() {
             return Ok(None);
         }
 

exon/exon-core/src/datasources/bed/config.rs → exon/exon-bed/src/config.rs

@@ -15,10 +15,9 @@
 use std::sync::Arc;
 
 use arrow::datatypes::SchemaRef;
+use exon_common::DEFAULT_BATCH_SIZE;
 use object_store::ObjectStore;
 
-use crate::datasources::DEFAULT_BATCH_SIZE;
-
 /// Configuration for a BED datasource.
 #[derive(Debug)]
 pub struct BEDConfig {

exon/exon-bed/src/lib.rs

@@ -0,0 +1,23 @@
+// 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.
+
+mod array_builder;
+mod batch_reader;
+mod bed_record_builder;
+mod config;
+
+pub use array_builder::BEDArrayBuilder;
+pub use array_builder::BEDSchemaBuilder;
+pub use batch_reader::BatchReader;
+pub use config::BEDConfig;

exon/exon-core/Cargo.toml

@@ -19,6 +19,7 @@ byteorder = {version = "1.5.0", optional = true}
 bytes = "1.5.0"
 datafusion = {workspace = true}
 exon-bam = {path = "../exon-bam", version = "0.3.9"}
+exon-bed = {path = "../exon-bed", version = "0.3.9"}
 exon-common = {path = "../exon-common", version = "0.3.9"}
 exon-fasta = {path = "../exon-fasta", version = "0.3.9"}
 exon-fastq = {path = "../exon-fastq", version = "0.3.9"}

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

@@ -21,11 +21,10 @@ use datafusion::{
     },
     error::DataFusionError,
 };
+use exon_bed::{BEDConfig, BatchReader};
 use futures::{StreamExt, TryStreamExt};
 use tokio_util::io::StreamReader;
 
-use super::{batch_reader::BatchReader, config::BEDConfig};
-
 /// Implements a datafusion `FileOpener` for BED files.
 pub struct BEDOpener {
     /// The configuration for the file scan.

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

@@ -16,16 +16,11 @@
 //!
 //! This module provides functionality for working with BED files as a data source.
 
-mod array_builder;
-mod batch_reader;
-mod bed_record_builder;
-mod config;
 mod file_opener;
 mod scanner;
 
 /// Table provider for BED files.
 pub mod table_provider;
 
-pub use self::config::BEDConfig;
 pub use self::file_opener::BEDOpener;
 pub use self::scanner::BEDScan;

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

@@ -25,10 +25,11 @@ use datafusion::{
         Partitioning, SendableRecordBatchStream,
     },
 };
+use exon_bed::BEDConfig;
 
 use crate::datasources::ExonFileScanConfig;
 
-use super::{config::BEDConfig, file_opener::BEDOpener};
+use super::file_opener::BEDOpener;
 
 #[derive(Debug, Clone)]
 /// Implements a datafusion `ExecutionPlan` for BED files.

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

@@ -35,10 +35,11 @@ use datafusion::{
     physical_plan::{empty::EmptyExec, ExecutionPlan},
     prelude::Expr,
 };
+use exon_bed::BEDSchemaBuilder;
 use exon_common::TableSchema;
 use futures::TryStreamExt;
 
-use super::{array_builder::BEDSchemaBuilder, BEDScan};
+use super::BEDScan;
 
 #[derive(Debug, Clone)]
 /// Configuration for a VCF listing table