chore: Switch to using noodles group (#459)

Co-authored-by: varfish-bot <[email protected]>

Cargo.toml

@@ -38,13 +38,6 @@ indexmap = { version = "2.2", features = ["serde"] }
 indicatif = { version = "0.17", features = ["rayon"] }
 itertools = "0.13.0"
 log = "0.4"
-noodles-bed = "0.13"
-noodles-bgzf = "0.30"
-noodles-core = "0.15"
-noodles-csi = "0.35"
-noodles-gff = "0.33.0"
-noodles-tabix = "0.41"
-noodles-vcf = "0.57"
 pbjson = "0.6"
 pbjson-types = "0.6"
 prost = "0.12"
@@ -53,13 +46,17 @@ rocksdb = { version = "0.22", features = ["multi-threaded-cf"] }
 rocksdb-utils-lookup = "0.4"
 rustc-hash = "1.1.0"
 serde = { version = "1.0", features = ["derive"] }
-serde_json = { version = "1.0", features=["preserve_order"] }
-serde_with = { version = "3.6", features=["alloc", "macros", "indexmap_2"], default-features = false }
+serde_json = { version = "1.0", features = ["preserve_order"] }
+serde_with = { version = "3.6", features = ["alloc", "macros", "indexmap_2"], default-features = false }
 strum = { version = "0.26", features = ["strum_macros", "derive"] }
 thiserror = "1.0"
 tracing = "0.1"
 tracing-subscriber = "0.3"
 
+[dependencies.noodles]
+version = "0.75.0"
+features = ["bed", "bgzf", "core", "csi", "gff", "tabix", "vcf"]
+
 [build-dependencies]
 anyhow = "1.0"
 pbjson-build = "0.6"

src/common/keys.rs

@@ -92,7 +92,7 @@ impl Var {
     }
 
     /// Create for all alternate alleles from the given VCF record.
-    pub fn from_vcf_allele(value: &noodles_vcf::variant::RecordBuf, allele_no: usize) -> Self {
+    pub fn from_vcf_allele(value: &noodles::vcf::variant::RecordBuf, allele_no: usize) -> Self {
         let chrom = value.reference_sequence_name().to_string();
         let pos: usize = value
             .variant_start()

src/common/noodles.rs

@@ -2,13 +2,11 @@
 
 use std::str::FromStr;
 
-use noodles_vcf::variant::record_buf::info::field;
+use noodles::vcf::variant::record_buf::info::field;
+use noodles::vcf::variant::RecordBuf as VcfRecord;
 
 /// Extract a `String` field from a record.
-pub fn get_string(
-    record: &noodles_vcf::variant::RecordBuf,
-    name: &str,
-) -> Result<String, anyhow::Error> {
+pub fn get_string(record: &VcfRecord, name: &str) -> Result<String, anyhow::Error> {
     if let Some(Some(field::Value::String(v))) = record.info().get(name) {
         Ok(v.to_string())
     } else if let Some(Some(field::Value::Array(field::value::Array::String(vs)))) =
@@ -21,18 +19,15 @@ pub fn get_string(
 }
 
 /// Extract a flag field from a record.
-pub fn get_flag(
-    record: &noodles_vcf::variant::RecordBuf,
-    name: &str,
-) -> Result<bool, anyhow::Error> {
+pub fn get_flag(record: &VcfRecord, name: &str) -> Result<bool, anyhow::Error> {
     Ok(matches!(
         record.info().get(name),
         Some(Some(field::Value::Flag))
     ))
 }
 
 /// Extract an `i32` field from a record.
-pub fn get_i32(record: &noodles_vcf::variant::RecordBuf, name: &str) -> Result<i32, anyhow::Error> {
+pub fn get_i32(record: &VcfRecord, name: &str) -> Result<i32, anyhow::Error> {
     if let Some(Some(field::Value::Integer(v))) = record.info().get(name) {
         Ok(*v)
     } else if let Some(Some(field::Value::Array(field::value::Array::Integer(vs)))) =
@@ -45,7 +40,7 @@ pub fn get_i32(record: &noodles_vcf::variant::RecordBuf, name: &str) -> Result<i
 }
 
 /// Extract an `f32` field from a record.
-pub fn get_f32(record: &noodles_vcf::variant::RecordBuf, name: &str) -> Result<f32, anyhow::Error> {
+pub fn get_f32(record: &VcfRecord, name: &str) -> Result<f32, anyhow::Error> {
     if let Some(Some(field::Value::Float(v))) = record.info().get(name) {
         Ok(*v)
     } else if let Some(Some(field::Value::Array(field::value::Array::Float(vs)))) =
@@ -60,10 +55,7 @@ pub fn get_f32(record: &noodles_vcf::variant::RecordBuf, name: &str) -> Result<f
 /// Extract an `Vec<String>` field from record with an array field.
 ///
 /// This is different than parsing the histograms from pipe-separated strings.
-pub fn get_vec_str(
-    record: &noodles_vcf::variant::RecordBuf,
-    name: &str,
-) -> Result<Vec<String>, anyhow::Error> {
+pub fn get_vec_str(record: &VcfRecord, name: &str) -> Result<Vec<String>, anyhow::Error> {
     if let Some(Some(field::Value::Array(field::value::Array::String(vs)))) =
         record.info().get(name)
     {
@@ -76,10 +68,7 @@ pub fn get_vec_str(
 /// Extract an `Vec<i32>` field from record with an array field.
 ///
 /// This is different than parsing the histograms from pipe-separated strings.
-pub fn get_vec_i32(
-    record: &noodles_vcf::variant::RecordBuf,
-    name: &str,
-) -> Result<Vec<i32>, anyhow::Error> {
+pub fn get_vec_i32(record: &VcfRecord, name: &str) -> Result<Vec<i32>, anyhow::Error> {
     if let Some(Some(field::Value::Array(field::value::Array::Integer(vs)))) =
         record.info().get(name)
     {
@@ -90,10 +79,7 @@ pub fn get_vec_i32(
 }
 
 /// Extract an `Vec<FromStr>` field from a record encoded as a pipe symbol separated string.
-pub fn get_vec<T>(
-    record: &noodles_vcf::variant::RecordBuf,
-    name: &str,
-) -> Result<Vec<T>, anyhow::Error>
+pub fn get_vec<T>(record: &VcfRecord, name: &str) -> Result<Vec<T>, anyhow::Error>
 where
     T: FromStr,
 {
@@ -109,10 +95,7 @@ where
 
 /// Extract an `Vec<Vec<FromStr>>` field from a record encoded as a list of pipe symbol
 /// separated string.
-pub fn get_vec_vec<T>(
-    record: &noodles_vcf::variant::RecordBuf,
-    name: &str,
-) -> Result<Vec<T>, anyhow::Error>
+pub fn get_vec_vec<T>(record: &VcfRecord, name: &str) -> Result<Vec<T>, anyhow::Error>
 where
     T: FromStr,
 {

src/db_utils/cli/copy.rs

@@ -59,12 +59,12 @@ fn copy_cf_bed(
 ) -> Result<(), anyhow::Error> {
     let mut reader = File::open(path_bed)
         .map(BufReader::new)
-        .map(noodles_bed::Reader::new)?;
+        .map(noodles::bed::Reader::new)?;
 
     tracing::info!("  reading BED records...");
     let bed_records = reader
         .records::<3>()
-        .collect::<Result<Vec<noodles_bed::Record<3>>, _>>()?;
+        .collect::<Result<Vec<noodles::bed::Record<3>>, _>>()?;
     tracing::info!(
         "  will process {} BED records in parallel...",
         bed_records.len()