fix: update noodles group

Cargo.toml

@@ -37,11 +37,11 @@ indexmap = { version = "2.2", features = ["serde"] }
 indicatif = { version = "0.17", features = ["rayon"] }
 log = "0.4"
 noodles-bed = "0.12"
-noodles-bgzf = "0.26"
+noodles-bgzf = "0.29"
 noodles-core = "0.14"
-noodles-csi = "0.30"
-noodles-tabix = "0.36"
-noodles-vcf = "0.49"
+noodles-csi = "0.33"
+noodles-tabix = "0.39"
+noodles-vcf = "0.55"
 pbjson = "0.6"
 pbjson-types = "0.6"
 prost = "0.12"
@@ -58,6 +58,7 @@ tracing-subscriber = "0.3"
 rustc-hash = "1.1.0"
 noodles-gff = "0.27.0"
 erased-serde = "0.4.2"
+itertools = "0.11.0"
 
 [build-dependencies]
 prost-build = "0.12"

src/common/keys.rs

@@ -92,19 +92,19 @@ impl Var {
     }
 
     /// Create for all alternate alleles from the given VCF record.
-    pub fn from_vcf_allele(value: &noodles_vcf::Record, allele_no: usize) -> Self {
-        let chrom = match value.chromosome() {
-            noodles_vcf::record::Chromosome::Name(name)
-            | noodles_vcf::record::Chromosome::Symbol(name) => name.to_owned(),
-        };
-        let pos: usize = value.position().into();
-        let pos = pos as i32;
+    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()
+            .expect("Telomeric breakends not supported")
+            .get();
+        let pos = i32::try_from(pos).unwrap();
         let reference = value.reference_bases().to_string();
         Var {
             chrom,
             pos,
             reference,
-            alternative: value.alternate_bases()[allele_no].to_string(),
+            alternative: value.alternate_bases().as_ref()[allele_no].to_string(),
         }
     }
 }

src/common/noodles.rs

@@ -2,14 +2,17 @@
 
 use std::str::FromStr;
 
-use noodles_vcf::record::info::field;
+use noodles_vcf::variant::record_buf::info::field;
 
 /// Extract a `String` field from a record.
-pub fn get_string(record: &noodles_vcf::Record, name: &str) -> Result<String, anyhow::Error> {
-    if let Some(Some(field::Value::String(v))) = record.info().get(&field::Key::from_str(name)?) {
+pub fn get_string(
+    record: &noodles_vcf::variant::RecordBuf,
+    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)))) =
-        record.info().get(&field::Key::from_str(name)?)
+        record.info().get(name)
     {
         Ok(vs.first().unwrap().as_ref().unwrap().to_string())
     } else {
@@ -18,19 +21,22 @@
 }
 
 /// Extract a flag field from a record.
-pub fn get_flag(record: &noodles_vcf::Record, name: &str) -> Result<bool, anyhow::Error> {
+pub fn get_flag(
+    record: &noodles_vcf::variant::RecordBuf,
+    name: &str,
+) -> Result<bool, anyhow::Error> {
     Ok(matches!(
-        record.info().get(&field::Key::from_str(name)?),
+        record.info().get(name),
         Some(Some(field::Value::Flag))
     ))
 }
 
 /// Extract an `i32` field from a record.
-pub fn get_i32(record: &noodles_vcf::Record, name: &str) -> Result<i32, anyhow::Error> {
-    if let Some(Some(field::Value::Integer(v))) = record.info().get(&field::Key::from_str(name)?) {
+pub fn get_i32(record: &noodles_vcf::variant::RecordBuf, 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)))) =
-        record.info().get(&field::Key::from_str(name)?)
+        record.info().get(name)
     {
         Ok(vs.first().unwrap().unwrap())
     } else {
@@ -39,11 +45,11 @@
 }
 
 /// Extract an `f32` field from a record.
-pub fn get_f32(record: &noodles_vcf::Record, name: &str) -> Result<f32, anyhow::Error> {
-    if let Some(Some(field::Value::Float(v))) = record.info().get(&field::Key::from_str(name)?) {
+pub fn get_f32(record: &noodles_vcf::variant::RecordBuf, 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)))) =
-        record.info().get(&field::Key::from_str(name)?)
+        record.info().get(name)
     {
         Ok(vs.first().unwrap().unwrap())
     } else {
@@ -54,9 +60,12 @@
 /// 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::Record, name: &str) -> Result<Vec<String>, anyhow::Error> {
+pub fn get_vec_str(
+    record: &noodles_vcf::variant::RecordBuf,
+    name: &str,
+) -> Result<Vec<String>, anyhow::Error> {
     if let Some(Some(field::Value::Array(field::value::Array::String(vs)))) =
-        record.info().get(&field::Key::from_str(name)?)
+        record.info().get(name)
     {
         Ok(vs.iter().flatten().cloned().collect())
     } else {
@@ -67,9 +76,12 @@
 /// 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::Record, name: &str) -> Result<Vec<i32>, anyhow::Error> {
+pub fn get_vec_i32(
+    record: &noodles_vcf::variant::RecordBuf,
+    name: &str,
+) -> Result<Vec<i32>, anyhow::Error> {
     if let Some(Some(field::Value::Array(field::value::Array::Integer(vs)))) =
-        record.info().get(&field::Key::from_str(name)?)
+        record.info().get(name)
     {
         Ok(vs.iter().flatten().cloned().collect())
     } else {
@@ -78,11 +90,14 @@
 }
 
 /// Extract an `Vec<FromStr>` field from a record encoded as a pipe symbol separated string.
-pub fn get_vec<T>(record: &noodles_vcf::Record, name: &str) -> Result<Vec<T>, anyhow::Error>
+pub fn get_vec<T>(
+    record: &noodles_vcf::variant::RecordBuf,
+    name: &str,
+) -> Result<Vec<T>, anyhow::Error>
 where
     T: FromStr,
 {
-    if let Some(Some(field::Value::String(v))) = record.info().get(&field::Key::from_str(name)?) {
+    if let Some(Some(field::Value::String(v))) = record.info().get(name) {
         v.split('|')
             .map(|s| s.parse())
             .collect::<Result<Vec<_>, _>>()
@@ -94,12 +109,15 @@
 
 /// 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::Record, name: &str) -> Result<Vec<T>, anyhow::Error>
+pub fn get_vec_vec<T>(
+    record: &noodles_vcf::variant::RecordBuf,
+    name: &str,
+) -> Result<Vec<T>, anyhow::Error>
 where
     T: FromStr,
 {
     if let Some(Some(field::Value::Array(field::value::Array::String(value)))) =
-        record.info().get(&field::Key::from_str(name)?)
+        record.info().get(name)
     {
         Ok(value
             .iter()

src/dbsnp/cli/import.rs

@@ -8,6 +8,7 @@ use clap::Parser;
 use indicatif::ParallelProgressIterator;
 use noodles_csi::BinningIndex as _;
 use noodles_vcf::header::record;
+use noodles_vcf::variant::RecordBuf;
 use prost::Message;
 use rayon::prelude::{IntoParallelRefIterator, ParallelIterator};
 
@@ -105,7 +106,7 @@ fn process_window(
     let cf_dbsnp = db.cf_handle(&args.cf_name).unwrap();
     let cf_dbsnp_by_rsid = db.cf_handle(&args.cf_name_by_rsid).unwrap();
     let mut reader =
-        noodles_vcf::indexed_reader::Builder::default().build_from_path(&args.path_in_vcf)?;
+        noodles_vcf::io::indexed_reader::Builder::default().build_from_path(&args.path_in_vcf)?;
     let header = reader.read_header()?;
 
     let raw_region = format!("{}:{}-{}", chrom, begin + 1, end);
@@ -130,10 +131,10 @@ fn process_window(
     // exist).
     if let Some(query) = query {
         for result in query {
-            let vcf_record = result?;
+            let vcf_record = RecordBuf::try_from_variant_record(&header, &result?)?;
 
             // Process each alternate allele into one record.
-            for allele_no in 0..vcf_record.alternate_bases().len() {
+            for allele_no in 0..vcf_record.alternate_bases().as_ref().len() {
                 let key_buf: Vec<u8> =
                     common::keys::Var::from_vcf_allele(&vcf_record, allele_no).into();
                 let record = dbsnp::pbs::Record::from_vcf_allele(&vcf_record, allele_no)?;
@@ -158,7 +159,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error>
     tracing::info!("Opening dbSNP VCF file...");
     let before_loading = std::time::Instant::now();
     let mut reader_vcf =
-        noodles_vcf::indexed_reader::Builder::default().build_from_path(&args.path_in_vcf)?;
+        noodles_vcf::io::indexed_reader::Builder::default().build_from_path(&args.path_in_vcf)?;
     let header = reader_vcf.read_header()?;
     let dbsnp_reference = if let record::value::Collection::Unstructured(values) = header
         .other_records()

src/dbsnp/pbs.rs

@@ -1,28 +1,30 @@
 //! Data structures for (de-)serialization as generated by `prost-build`.
 
-use std::str::FromStr;
+use noodles_vcf::variant::record::AlternateBases;
 
 pub use crate::pbs::dbsnp::Record;
-use noodles_vcf::record::info::field;
+use noodles_vcf::variant::record_buf::info::field;
 
 impl Record {
     /// Creates a new `Record` from a VCF record and allele number.
     pub fn from_vcf_allele(
-        record: &noodles_vcf::record::Record,
+        record: &noodles_vcf::variant::RecordBuf,
         allele_no: usize,
     ) -> Result<Self, anyhow::Error> {
-        let chrom = record.chromosome().to_string();
-        let pos: usize = record.position().into();
-        let pos: i32 = pos.try_into()?;
+        let chrom = record.reference_sequence_name().to_string();
+        let pos: usize = record
+            .variant_start()
+            .expect("Telomeric breakends not supported")
+            .get();
+        let pos: i32 = i32::try_from(pos)?;
         let ref_allele = record.reference_bases().to_string();
         let alt_allele = record
             .alternate_bases()
-            .get(allele_no)
-            .ok_or_else(|| anyhow::anyhow!("no such allele: {}", allele_no))?
+            .iter()
+            .nth(allele_no)
+            .ok_or_else(|| anyhow::anyhow!("no such allele: {}", allele_no))??
             .to_string();
-        let rs_id = if let Some(Some(field::Value::Integer(rs))) =
-            record.info().get(&field::Key::from_str("RS")?)
-        {
+        let rs_id = if let Some(Some(field::Value::Integer(rs))) = record.info().get("RS") {
             *rs
         } else {
             anyhow::bail!("no rs id in dbSNP record")