dep: update rand dependency and update api

Author: noamteyssier

Cargo.toml

@@ -16,14 +16,13 @@ bitnuc = "0.2.8"
 bytemuck = "1.21.0"
 byteorder = "1.5.0"
 memmap2 = "0.9.5"
-rand = { version = "0.8.5", features = ["small_rng"] }
+rand = { version = "0.9.1", features = ["small_rng"] }
 thiserror = "2.0.8"
 zstd = { version = "0.13.3", features = ["zstdmt"] }
 
 [dev-dependencies]
-nucgen = "0.1.1"
-rand = "0.8.5"
-niffler = "2.6.0"
+nucgen = "0.2.0"
+niffler = "3.0.0"
 seq_io = "0.3.2"
 parking_lot = "0.12.3"
 itoa = "1.0.14"

examples/parallel_processing.rs

@@ -120,7 +120,7 @@ fn write_single(binseq_path: &str, num_seq: usize, seq_size: usize) -> Result<()
 
     // Write the binary sequence
     let mut sequence = Sequence::new();
-    let mut rng = rand::thread_rng();
+    let mut rng = rand::rng();
     for _ in 0..num_seq {
         sequence.fill_buffer(&mut rng, seq_size);
         if !writer.write_nucleotides(0, sequence.bytes())? {
@@ -146,7 +146,7 @@ fn write_paired(binseq_path: &str, num_seq: usize, r1_size: usize, r2_size: usiz
     // Write the binary sequence
     let mut r1 = Sequence::new();
     let mut r2 = Sequence::new();
-    let mut rng = rand::thread_rng();
+    let mut rng = rand::rng();
     for _ in 0..num_seq {
         r1.fill_buffer(&mut rng, r1_size);
         r2.fill_buffer(&mut rng, r2_size);

src/policy.rs

@@ -84,7 +84,7 @@ impl Policy {
         for &n in sequence {
             ibuf.push(match n {
                 b'A' | b'C' | b'G' | b'T' => n,
-                _ => match rng.gen_range(0..4) {
+                _ => match rng.random_range(0..4) {
                     0 => b'A',
                     1 => b'C',
                     2 => b'G',