use xvcf-rs in index

Cargo.toml

@@ -15,17 +15,18 @@ path = "src/main.rs"
 
 [dependencies]
 rand = "0.8.5"
-smartstring = {version = "1.0.1", optional = true }
-smol_str = {version = "0.2.0", optional = true }
-compact_str = {version = "0.7.0", optional = true }
-kstring = {version = "2.0.0", optional = true }
-noodles = {version = "0.45.0"}
+smartstring = { version = "1.0.1", optional = true }
+smol_str = { version = "0.2.0", optional = true }
+compact_str = { version = "0.7.0", optional = true }
+kstring = { version = "2.0.0", optional = true }
+noodles = { version = "0.51.0" }
 flate2 = "1.0.26"
-clap = {version="4.2.7", features=['derive']}
+clap = { version = "4.2.7", features = ['derive'] }
 env_logger = "0.10.0"
 log = "0.4.19"
 linear-map = "1.2.0"
 hashbrown = "0.14.0"
+xvcf = { version = "0.1.1", git = "https://github.com/brentp/xvcf-rs" }
 
 [features]
 default = ["bed", "vcf", "bcf", "csi", "core", "bam", "sam", "bgzf"]
@@ -43,12 +44,11 @@ dyn_positioned = []
 
 [dev-dependencies]
 criterion = { version = "0.4", features = ["html_reports"] }
-clap = {version = "4.2.7", features=["derive"]}
+clap = { version = "4.2.7", features = ["derive"] }
 
 [[bench]]
 name = "random_intervals"
 harness = false
 
 [profile.release]
 lto = true
-

src/bedder_vcf.rs

@@ -2,55 +2,36 @@ use crate::position::{Field, FieldError, Position, Positioned, Value};
 use crate::string::String;
 use noodles::bcf;
 use noodles::vcf::{self, record::Chromosome};
-use std::io::{self, BufRead};
+use std::io::{self, BufRead, Read};
 use std::result;
 use vcf::record::info::field;
 use vcf::record::QualityScore;
 pub use vcf::Record;
-
-pub trait VCFReader {
-    fn read_record(&mut self, header: &vcf::Header, v: &mut vcf::Record) -> io::Result<usize>;
-    // fn queryable
-}
-
-pub enum VCF<R> {
-    VCF(vcf::Reader<R>),
-    IndexedVCF(vcf::indexed_reader::IndexedReader<R>),
-    BCF(bcf::Reader<R>),
-    IndexedBCF(bcf::indexed_reader::IndexedReader<R>),
-}
-
-impl<R> VCFReader for VCF<R>
-where
-    R: BufRead,
-{
-    fn read_record(&mut self, header: &vcf::Header, v: &mut vcf::Record) -> io::Result<usize> {
-        match self {
-            VCF::VCF(r) => r.read_record(header, v),
-            VCF::IndexedVCF(r) => r.read_record(header, v),
-            VCF::BCF(r) => r.read_record(header, v),
-            VCF::IndexedBCF(r) => r.read_record(header, v),
-        }
-    }
-}
+pub use xvcf;
 
 pub struct BedderVCF<R> {
-    reader: VCF<R>,
-    header: vcf::Header,
+    reader: xvcf::Reader<R>,
     record_number: u64,
 }
 
-impl<R> BedderVCF<R> {
-    pub fn new(r: VCF<R>, header: vcf::Header) -> io::Result<BedderVCF<R>> {
+impl<R> BedderVCF<R>
+where
+    R: Read + 'static,
+{
+    pub fn new(r: xvcf::Reader<R>) -> io::Result<BedderVCF<R>> {
         let v = BedderVCF {
             reader: r,
-            header,
             record_number: 0,
         };
         Ok(v)
     }
 }
 
+pub fn from_reader<R: Read>(r: Box<R>) -> io::Result<BedderVCF<R>> {
+    let reader = xvcf::Reader::from_reader(r, None)?;
+    BedderVCF::new(reader)
+}
+
 fn match_info_value(info: &vcf::record::Info, name: &str) -> result::Result<Value, FieldError> {
     //let info = record.info();
     let key: vcf::record::info::field::Key = name
@@ -153,15 +134,15 @@ impl Positioned for vcf::record::Record {
 
 impl<R> crate::position::PositionedIterator for BedderVCF<R>
 where
-    R: BufRead,
+    R: Read + 'static,
 {
     fn next_position(
         &mut self,
         _q: Option<&crate::position::Position>,
     ) -> Option<std::result::Result<Position, std::io::Error>> {
         let mut v = vcf::Record::default();
 
-        match self.reader.read_record(&self.header, &mut v) {
+        match self.reader.next_record(&self.reader.header(), &mut v) {
             Ok(0) => None, // EOF
             Ok(_) => {
                 self.record_number += 1;