Merge branch 'ar/gh-178' into 'master'

[bug] Tabix indices don't load

See merge request machine-learning/modkit!176

Cargo.toml

@@ -31,7 +31,7 @@ log4rs = { version = "1.2.0", features = ["file_appender", "json_encoder"] }
 memchr = "2.6.4"
 ndarray = "0.15.6"
 nom = "7.1.3"
-noodles = { version = "0.69.0", features = ["tabix", "core", "bgzf", "csi", "tabix"] }
+noodles = { version = "0.50.0", features = ["tabix", "core", "bgzf", "csi", "tabix"] }
 prettytable-rs = "0.10.0"
 pulp = "0.18.10"
 rand = "0.8.5"

src/dmr/tabix.rs

@@ -7,10 +7,9 @@ use std::path::{Path, PathBuf};
 use anyhow::{anyhow, bail, Context};
 use log::debug;
 use noodles::csi::{
-    binning_index::index::reference_sequence::bin::Chunk as IndexChunk,
-    BinningIndex,
+    index::reference_sequence::bin::Chunk as IndexChunk, Index as CsiIndex,
 };
-use noodles::tabix::Index as CsiIndex;
+
 use rayon::prelude::*;
 use rustc_hash::FxHashMap;
 

src/dmr/util.rs

@@ -15,7 +15,7 @@ use log_once::debug_once;
 use nom::character::complete::one_of;
 use nom::multi::many0;
 use nom::IResult;
-use noodles::csi::binning_index::index::reference_sequence::bin::Chunk as IndexChunk;
+use noodles::csi::index::reference_sequence::bin::Chunk as IndexChunk;
 use rustc_hash::{FxHashMap, FxHashSet};
 
 use crate::dmr::tabix::MultiSampleIndex;
@@ -503,7 +503,7 @@ mod dmr_util_tests {
     use std::collections::BTreeSet;
 
     use noodles::bgzf::VirtualPosition;
-    use noodles::csi::binning_index::index::reference_sequence::bin::Chunk as IndexChunk;
+    use noodles::csi::index::reference_sequence::bin::Chunk as IndexChunk;
 
     use crate::dmr::util::{parse_roi_bed, DmrInterval, ProtoIndexChunk};
     use crate::position_filter::Iv;