opt build

Cargo.lock

@@ -29,7 +29,7 @@ version = "0.7.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "891477e0c6a8957309ee5c45a6368af3ae14bb510732d2684ffa19af310920f9"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.15",
  "once_cell",
  "version_check",
 ]
@@ -42,10 +42,10 @@ checksum = "e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011"
 dependencies = [
  "cfg-if",
  "const-random",
- "getrandom",
+ "getrandom 0.2.15",
  "once_cell",
  "version_check",
- "zerocopy",
+ "zerocopy 0.7.35",
 ]
 
 [[package]]
@@ -1207,7 +1207,7 @@ version = "0.1.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f9d839f2a20b0aee515dc581a6172f2321f96cab76c1a38a4c584a194955390e"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.15",
  "once_cell",
  "tiny-keccak",
 ]
@@ -1964,7 +1964,7 @@ dependencies = [
  "num-complex",
  "num-traits",
  "opimps",
- "rand",
+ "rand 0.8.5",
  "rand_distr",
 ]
 
@@ -2081,7 +2081,19 @@ checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7"
 dependencies = [
  "cfg-if",
  "libc",
- "wasi",
+ "wasi 0.11.0+wasi-snapshot-preview1",
+]
+
+[[package]]
+name = "getrandom"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "43a49c392881ce6d5c3b8cb70f98717b7c07aabbdff06687b9030dbfbe2725f8"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "wasi 0.13.3+wasi-0.2.2",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -2912,8 +2924,8 @@ version = "0.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "636860251af8963cc40f6b4baadee105f02e21b28131d76eba8e40ce84ab8064"
 dependencies = [
- "rand",
- "rand_chacha",
+ "rand 0.8.5",
+ "rand_chacha 0.3.1",
 ]
 
 [[package]]
@@ -3080,7 +3092,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2886843bf800fba2e3377cff24abf6379b4c4d5c6681eaf9ea5b0d15090450bd"
 dependencies = [
  "libc",
- "wasi",
+ "wasi 0.11.0+wasi-snapshot-preview1",
  "windows-sys 0.52.0",
 ]
 
@@ -3101,7 +3113,7 @@ dependencies = [
  "num-complex",
  "num-rational",
  "num-traits",
- "rand",
+ "rand 0.8.5",
  "rand_distr",
  "simba",
  "typenum",
@@ -3252,9 +3264,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-fasta"
-version = "0.47.0"
+version = "0.48.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ad6daab7b0475167724742ce5e799de6aaac19c75ed1b56d0040ef1dab6ca079"
+checksum = "ce052e3ec1623aac185890eac7c6c76bca100876dce3507a58fbb29957ba1af2"
 dependencies = [
  "bstr",
  "bytes",
@@ -3365,7 +3377,7 @@ checksum = "a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9"
 dependencies = [
  "num-integer",
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -3703,10 +3715,9 @@ dependencies = [
  "locale_config",
  "log",
  "logtest",
- "nix 0.29.0",
  "noodles-core 0.16.0",
  "noodles-csi 0.43.0",
- "noodles-fasta 0.47.0",
+ "noodles-fasta 0.48.0",
  "noodles-gff 0.43.0",
  "num-format",
  "pandora_lib_assembler",
@@ -3714,9 +3725,8 @@ dependencies = [
  "pandora_lib_scan",
  "pandora_lib_variants",
  "podders",
- "pty-process",
  "ptyprocess",
- "rand",
+ "rand 0.9.0",
  "rayon",
  "regex",
  "rusqlite",
@@ -3747,7 +3757,7 @@ dependencies = [
  "indicatif-log-bridge",
  "log",
  "pandora_lib_graph",
- "rand",
+ "rand 0.8.5",
  "rayon",
  "rust-htslib 0.49.0",
  "serde",
@@ -3923,7 +3933,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "48e4cc64c2ad9ebe670cb8fd69dd50ae301650392e81c05f9bfcb2d5bdbc24b0"
 dependencies = [
  "phf_shared",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -4072,7 +4082,7 @@ version = "0.2.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04"
 dependencies = [
- "zerocopy",
+ "zerocopy 0.7.35",
 ]
 
 [[package]]
@@ -4169,16 +4179,6 @@ dependencies = [
  "syn 1.0.109",
 ]
 
-[[package]]
-name = "pty-process"
-version = "0.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8749b545e244c90bf74a5767764cc2194f1888bb42f84015486a64c82bea5cc0"
-dependencies = [
- "libc",
- "rustix",
-]
-
 [[package]]
 name = "ptyprocess"
 version = "0.4.1"
@@ -4250,8 +4250,19 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404"
 dependencies = [
  "libc",
- "rand_chacha",
- "rand_core",
+ "rand_chacha 0.3.1",
+ "rand_core 0.6.4",
+]
+
+[[package]]
+name = "rand"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3779b94aeb87e8bd4e834cee3650289ee9e0d5677f976ecdb6d219e5f4f6cd94"
+dependencies = [
+ "rand_chacha 0.9.0",
+ "rand_core 0.9.0",
+ "zerocopy 0.8.17",
 ]
 
 [[package]]
@@ -4261,7 +4272,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88"
 dependencies = [
  "ppv-lite86",
- "rand_core",
+ "rand_core 0.6.4",
+]
+
+[[package]]
+name = "rand_chacha"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb"
+dependencies = [
+ "ppv-lite86",
+ "rand_core 0.9.0",
 ]
 
 [[package]]
@@ -4270,7 +4291,17 @@ version = "0.6.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.15",
+]
+
+[[package]]
+name = "rand_core"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b08f3c9802962f7e1b25113931d94f43ed9725bebc59db9d0c3e9a23b67e15ff"
+dependencies = [
+ "getrandom 0.3.1",
+ "zerocopy 0.8.17",
 ]
 
 [[package]]
@@ -4280,7 +4311,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32cb0b9bc82b0a0876c2dd994a7e7a2683d3e7390ca40e6886785ef0c7e3ee31"
 dependencies = [
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -4330,7 +4361,7 @@ version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ba009ff324d1fc1b900bd1fdb31564febe58a8ccc8a6fdbb93b543d33b13ca43"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.15",
  "libredox",
  "thiserror 1.0.69",
 ]
@@ -4341,7 +4372,7 @@ version = "0.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dd6f9d3d47bdd2ad6945c5015a226ec6155d0bcdfd8f7cd29f86b71f8de99d2b"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.15",
  "libredox",
  "thiserror 2.0.9",
 ]
@@ -4450,7 +4481,7 @@ checksum = "c17fa4cb658e3583423e915b9f3acc01cceaee1860e33d59ebae66adc3a2dc0d"
 dependencies = [
  "cc",
  "cfg-if",
- "getrandom",
+ "getrandom 0.2.15",
  "libc",
  "spin",
  "untrusted",
@@ -4596,7 +4627,7 @@ dependencies = [
  "borsh",
  "bytes",
  "num-traits",
- "rand",
+ "rand 0.8.5",
  "rkyv",
  "serde",
  "serde_json",
@@ -4649,7 +4680,6 @@ checksum = "f93dc38ecbab2eb790ff964bb77fa94faf256fd3e73285fd7ba0903b76bedb85"
 dependencies = [
  "bitflags 2.6.0",
  "errno",
- "itoa",
  "libc",
  "linux-raw-sys",
  "windows-sys 0.59.0",
@@ -5111,7 +5141,7 @@ dependencies = [
  "approx",
  "nalgebra",
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -5310,7 +5340,7 @@ checksum = "9a8a559c81686f576e8cd0290cd2a24a2a9ad80c98b3478856500fcbd7acd704"
 dependencies = [
  "cfg-if",
  "fastrand",
- "getrandom",
+ "getrandom 0.2.15",
  "once_cell",
  "rustix",
  "windows-sys 0.59.0",
@@ -6222,11 +6252,11 @@ dependencies = [
 
 [[package]]
 name = "uuid"
-version = "1.11.0"
+version = "1.13.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f8c5f0a0af699448548ad1a2fbf920fb4bee257eae39953ba95cb84891a0446a"
+checksum = "ced87ca4be083373936a67f8de945faa23b6b42384bd5b64434850802c6dccd0"
 dependencies = [
- "getrandom",
+ "getrandom 0.3.1",
  "serde",
 ]
 
@@ -6287,6 +6317,15 @@ version = "0.11.0+wasi-snapshot-preview1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
+[[package]]
+name = "wasi"
+version = "0.13.3+wasi-0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "26816d2e1a4a36a2940b96c5296ce403917633dff8f3440e9b236ed6f6bacad2"
+dependencies = [
+ "wit-bindgen-rt",
+]
+
 [[package]]
 name = "wasm-bindgen"
 version = "0.2.99"
@@ -6709,6 +6748,15 @@ version = "0.0.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d135d17ab770252ad95e9a872d365cf3090e3be864a34ab46f48555993efc904"
 
+[[package]]
+name = "wit-bindgen-rt"
+version = "0.33.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3268f3d866458b787f390cf61f4bbb563b922d091359f9608842999eaee3943c"
+dependencies = [
+ "bitflags 2.6.0",
+]
+
 [[package]]
 name = "write16"
 version = "1.0.0"
@@ -6799,7 +6847,16 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0"
 dependencies = [
  "byteorder",
- "zerocopy-derive",
+ "zerocopy-derive 0.7.35",
+]
+
+[[package]]
+name = "zerocopy"
+version = "0.8.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "aa91407dacce3a68c56de03abe2760159582b846c6a4acd2f456618087f12713"
+dependencies = [
+ "zerocopy-derive 0.8.17",
 ]
 
 [[package]]
@@ -6813,6 +6870,17 @@ dependencies = [
  "syn 2.0.95",
 ]
 
+[[package]]
+name = "zerocopy-derive"
+version = "0.8.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "06718a168365cad3d5ff0bb133aad346959a2074bd4a85c121255a11304a8626"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.95",
+]
+
 [[package]]
 name = "zerofrom"
 version = "0.1.5"

Cargo.toml

@@ -7,7 +7,7 @@ edition = "2021"
 log = "^0.4.22"
 env_logger = "^0.11.3"
 anyhow = "1.0.86"
-glob = "0.3.1"
+glob = "0.3.2"
 pandora_lib_bindings = { git = "https://git.t0m4.fr/Thomas/pandora_lib_bindings.git" }
 pandora_lib_scan = { git = "https://git.t0m4.fr/Thomas/pandora_lib_scan.git" }
 pandora_lib_variants = { git = "https://git.t0m4.fr/Thomas/pandora_lib_variants.git" }
@@ -25,12 +25,10 @@ noodles-csi = "0.43.0"
 num-format = "0.4.4"
 locale_config = "0.3.0"
 byte-unit = "5.1.4"
-pty-process = "0.4.0"
-nix = { version = "0.29.0", features = ["term", "process" ] }
 expectrl = "0.7.1"
 ptyprocess = "0.4.1"
 duct = "0.13.7"
-uuid = { version = "1.10.0", features = ["v4"] }
+uuid = { version = "1.13.1", features = ["v4"] }
 rayon = "1.10.0"
 hashbrown = { version = "0.15.0", features = ["rayon"] }
 ctrlc = "3.4.4"
@@ -45,7 +43,7 @@ arrow = "54.0.0"
 bgzip = "0.3.1"
 tempfile = "3.14.0"
 dashmap = { version = "6.1.0", features = ["rayon", "serde"] }
-noodles-fasta = "0.47.0"
+noodles-fasta = "0.48.0"
 noodles-core = "0.16.0"
 blake3 = "1.5.5"
 charming = { version = "0.4.0", features = ["ssr"] }
@@ -53,5 +51,10 @@ rusqlite = { version = "0.32.1", features = ["chrono", "serde_json"] }
 dirs = "6.0.0"
 noodles-gff = "0.43.0"
 itertools = "0.14.0"
-rand = "0.8.5"
+rand = "0.9.0"
 tar = "0.4.43"
+
+[profile.dev]
+opt-level = 0
+debug = false
+

src/lib.rs

@@ -28,7 +28,7 @@ mod tests {
     use std::{collections::HashMap, fs, path::Path};
 
     use annotation::{vep::{VepLine, VEP}, Annotations};
-    use callers::{nanomonsv::nanomonsv_create_pon, savana::{Savana, SavanaCopyNumber, SavanaReadCounts}, severus::{Severus, SeverusSolo}};
+    use callers::{nanomonsv::nanomonsv_create_pon, savana::{Savana, SavanaReadCounts}, severus::{Severus, SeverusSolo}};
     use collection::{bam::{counts_at, counts_ins_at, nt_pileup, WGSBam, WGSBamStats}, pod5::{Pod5, Pod5Config}, Initialize, InitializeSolo, Version};
     use commands::{longphase::{LongphaseConfig, LongphaseHap, LongphaseModcallSolo, LongphasePhase}, modkit::{bed_methyl, ModkitConfig}};
     use functions::assembler::{Assembler, AssemblerConfig};
@@ -79,8 +79,9 @@ mod tests {
         Ok(())
     }
 
-    #[test_log::test]
+    #[test]
     fn bam() -> anyhow::Result<()> {
+        init();
         let bam_collection = bam::load_bam_collection("/data/longreads_basic_pipe");
 
         bam_collection
@@ -95,8 +96,9 @@ mod tests {
         Ok(())
     }
 
-    #[test_log::test]
+    #[test]
     fn vcf() -> anyhow::Result<()> {
+        init();
         let mut vcf_collection = VcfCollection::new("/data/longreads_basic_pipe");
         vcf_collection.sort_by_id();
         vcf_collection
@@ -109,8 +111,9 @@ mod tests {
 
     // pod5 view -I /data/run_data/20240903-CL/ARMEM-DG-N02_ASSJU-DG-N03/20240903_1428_1B_PAW47629_fc24c3cf/pod5/PAW47629_fc24c3cf_77b07847_0.pod5 | head -5000 | awk '{if(NR==1){print "target,"$0}else{print "subset_1.pod5,"$0}}' > /tmp/subset_ids.csv
     // pod5 subset /data/run_data/20240903-CL/ARMEM-DG-N02_ASSJU-DG-N03/20240903_1428_1B_PAW47629_fc24c3cf/pod5/PAW47629_fc24c3cf_77b07847_0.pod5 --csv /tmp/subset_ids.csv -o /data/test_suite/pod5/muxed/
-    #[test_log::test]
+    #[test]
     fn mux() -> anyhow::Result<()> {
+        init();
         let result_dir = "/data/test_suite/results".to_string();
         let cases = vec![
             FlowCellCase { id: "test_02".to_string(), time_point: "diag".to_string(), barcode: "02".to_string(), pod_dir: "/data/test_suite/pod5/muxed".into() },
@@ -136,8 +139,9 @@ mod tests {
     //     ClairS::new("test_a", "/data/test_data/subset.bam", "/data/test_data/subset_mrd.bam", config).run()
     // }
 
-    #[test_log::test]
+    #[test]
     fn nanomonsv() -> anyhow::Result<()> {
+        init();
         let id = "HAMROUNE";
         NanomonSV::initialize(id, Config::default())?.run()
     }
@@ -190,8 +194,9 @@ mod tests {
     }
 
     // export RUST_LOG="debug"
-    #[test_log::test]
+    #[test]
     fn run_t() -> anyhow::Result<()> {
+        init();
         // let config = CollectionsConfig::default();
         let config = CollectionsConfig { pod_dir: "/data/run_data".to_string(), ..Default::default() };
 
@@ -213,8 +218,9 @@ mod tests {
     //     bcftools_keep_pass(&i, &o, config).unwrap();
     // }
 
-    #[test_log::test]
+    #[test]
     fn bam_ok() -> anyhow::Result<()> {
+        init();
         let  collections = Collections::new(
             CollectionsConfig::default()
         )?;
@@ -228,8 +234,9 @@ mod tests {
         Ok(())
     }
 
-    #[test_log::test]
+    #[test]
     fn todo_assembler() -> anyhow::Result<()> {
+        init();
         let collections = Collections::new(
             CollectionsConfig::default()
         )?;