Update noodles crates to latest versions

- noodles-bam: 0.68 → 0.85
- noodles-sam: 0.65 → 0.81
- noodles-bgzf: 0.33 → 0.45
- noodles-core: 0.15 → 0.18

Updated MultithreadedReader path from bgzf:: to bgzf::io::
to match new API.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: jayhesselberth

Cargo.lock

@@ -15,10 +15,10 @@ path = "src/main.rs"
 
 [dependencies]
 # BAM/SAM parsing (pure Rust)
-noodles-bam = "0.68"
-noodles-sam = "0.65"
-noodles-bgzf = { version = "0.33", features = ["libdeflate"] }
-noodles-core = "0.15"
+noodles-bam = "0.85"
+noodles-sam = "0.81"
+noodles-bgzf = { version = "0.45", features = ["libdeflate"] }
+noodles-core = "0.18"
 
 # Parallelism
 rayon = "1.10"

Cargo.toml

@@ -51,7 +51,7 @@ impl Default for RecordBatch {
 /// BAM block reader that produces batches for parallel processing
 pub struct BamBlockReader {
     /// Underlying BGZF reader (multi-threaded for parallel decompression)
-    reader: bgzf::MultithreadedReader<File>,
+    reader: bgzf::io::MultithreadedReader<File>,
     /// BAM header
     header: sam::Header,
     /// Pre-computed ref_id -> chrom_id mapping
@@ -84,7 +84,7 @@ impl BamBlockReader {
         // Use multi-threaded BGZF reader for parallel decompression
         let worker_count =
             NonZeroUsize::new(threads.max(1)).expect("thread count must be positive");
-        let mut reader = bgzf::MultithreadedReader::with_worker_count(worker_count, file);
+        let mut reader = bgzf::io::MultithreadedReader::with_worker_count(worker_count, file);
 
         // Read BAM magic number
         let mut magic = [0u8; 4];

src/alignment/block_reader.rs

@@ -118,7 +118,7 @@ pub struct AlignmentReader {
 }
 
 enum ReaderInner {
-    Bam(bam::io::Reader<bgzf::MultithreadedReader<File>>),
+    Bam(bam::io::Reader<bgzf::io::MultithreadedReader<File>>),
     Sam(sam::io::Reader<std::io::BufReader<File>>),
 }
 
@@ -143,7 +143,7 @@ impl AlignmentReader {
             // Use multi-threaded BGZF reader for parallel decompression
             let worker_count =
                 NonZeroUsize::new(threads.max(1)).expect("thread count must be positive");
-            let bgzf_reader = bgzf::MultithreadedReader::with_worker_count(worker_count, file);
+            let bgzf_reader = bgzf::io::MultithreadedReader::with_worker_count(worker_count, file);
             let mut bam_reader = bam::io::Reader::from(bgzf_reader);
             let header = bam_reader.read_header()?;
 
@@ -186,7 +186,7 @@ impl AlignmentReader {
 
             let worker_count =
                 NonZeroUsize::new(threads.max(1)).expect("thread count must be positive");
-            let bgzf_reader = bgzf::MultithreadedReader::with_worker_count(worker_count, file);
+            let bgzf_reader = bgzf::io::MultithreadedReader::with_worker_count(worker_count, file);
             let mut bam_reader = bam::io::Reader::from(bgzf_reader);
             let header = bam_reader.read_header()?;