From 5f6e8340e01ad5afc656850a62d26631a19c04a0 Mon Sep 17 00:00:00 2001
From: Art Rand <art.rand@nanoporetech.com>
Date: Sat, 18 May 2024 17:50:39 +0000
Subject: [PATCH] [bug] Tabix indices don't load

---
 Cargo.toml       | 2 +-
 src/dmr/tabix.rs | 5 ++---
 src/dmr/util.rs  | 4 ++--
 3 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 4ab0e7e..500265e 100644
--- a/Cargo.toml
+++ b/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"
diff --git a/src/dmr/tabix.rs b/src/dmr/tabix.rs
index 8abd2e9..7dec2f1 100644
--- a/src/dmr/tabix.rs
+++ b/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;
 
diff --git a/src/dmr/util.rs b/src/dmr/util.rs
index 179fa33..8eb9c05 100644
--- a/src/dmr/util.rs
+++ b/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;