machete

Cargo.lock

@@ -553,7 +553,7 @@ dependencies = [
  "arrow-select 49.0.0",
  "num",
  "regex",
- "regex-syntax 0.8.5",
+ "regex-syntax",
 ]
 
 [[package]]
@@ -570,7 +570,7 @@ dependencies = [
  "memchr",
  "num",
  "regex",
- "regex-syntax 0.8.5",
+ "regex-syntax",
 ]
 
 [[package]]
@@ -809,12 +809,6 @@ dependencies = [
  "constant_time_eq",
 ]
 
-[[package]]
-name = "block"
-version = "0.1.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0d8c1fef690941d3e7788d328517591fecc684c084084702d6ff1641e993699a"
-
 [[package]]
 name = "block-buffer"
 version = "0.10.4"
@@ -1170,15 +1164,6 @@ dependencies = [
  "toml",
 ]
 
-[[package]]
-name = "conpty"
-version = "0.5.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b72b06487a0d4683349ad74d62e87ad639b09667082b3c495c5b6bab7d84b3da"
-dependencies = [
- "windows",
-]
-
 [[package]]
 name = "console"
 version = "0.15.10"
@@ -1340,7 +1325,7 @@ version = "3.4.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "90eeab0aa92f3f9b4e87f258c72b139c207d251f9cbc1080a0086b86a8870dd3"
 dependencies = [
- "nix 0.29.0",
+ "nix",
  "windows-sys 0.59.0",
 ]
 
@@ -1420,7 +1405,7 @@ dependencies = [
  "deno_unsync",
  "futures",
  "libc",
- "memoffset 0.9.1",
+ "memoffset",
  "parking_lot",
  "percent-encoding",
  "pin-project",
@@ -1683,19 +1668,6 @@ dependencies = [
  "regex",
 ]
 
-[[package]]
-name = "env_logger"
-version = "0.10.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580"
-dependencies = [
- "humantime",
- "is-terminal",
- "log",
- "regex",
- "termcolor",
-]
-
 [[package]]
 name = "env_logger"
 version = "0.11.6"
@@ -1725,18 +1697,6 @@ dependencies = [
  "windows-sys 0.59.0",
 ]
 
-[[package]]
-name = "expectrl"
-version = "0.7.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ede784925953fcab9a3351d5009bcb8d2b0c13e940924c88087e8e2ce0c4717a"
-dependencies = [
- "conpty",
- "nix 0.26.4",
- "ptyprocess",
- "regex",
-]
-
 [[package]]
 name = "exr"
 version = "1.73.0"
@@ -1795,15 +1755,6 @@ dependencies = [
  "simd-adler32",
 ]
 
-[[package]]
-name = "features"
-version = "0.10.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "83072b3c84e55f9d0c0ff36a4575d0fd2e543ae4a56e04e7f5a9222188d574e3"
-dependencies = [
- "bitflags 1.3.2",
-]
-
 [[package]]
 name = "filetime"
 version = "0.2.25"
@@ -1955,19 +1906,6 @@ dependencies = [
  "winapi",
 ]
 
-[[package]]
-name = "full"
-version = "0.3.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3eb4fedc7ed4eef621cda06d7b667b24bed97fee56fe7642d676ac409140163a"
-dependencies = [
- "num-complex",
- "num-traits",
- "opimps",
- "rand 0.8.5",
- "rand_distr",
-]
-
 [[package]]
 name = "funty"
 version = "2.0.0"
@@ -2937,19 +2875,6 @@ dependencies = [
  "serde",
 ]
 
-[[package]]
-name = "locale_config"
-version = "0.3.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "08d2c35b16f4483f6c26f0e4e9550717a2f6575bcd6f12a53ff0c490a94a6934"
-dependencies = [
- "lazy_static",
- "objc",
- "objc-foundation",
- "regex",
- "winapi",
-]
-
 [[package]]
 name = "lock_api"
 version = "0.4.12"
@@ -2965,19 +2890,6 @@ name = "log"
 version = "0.4.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
-dependencies = [
- "value-bag",
-]
-
-[[package]]
-name = "logtest"
-version = "2.0.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "eb3e43a8657c1d64516dcc9db8ca03826a4aceaf89d5ce1b37b59f6ff0e43026"
-dependencies = [
- "lazy_static",
- "log",
-]
 
 [[package]]
 name = "lzma-sys"
@@ -2990,24 +2902,6 @@ dependencies = [
  "pkg-config",
 ]
 
-[[package]]
-name = "malloc_buf"
-version = "0.0.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62bb907fe88d54d8d9ce32a3cceab4218ed2f6b7d35617cafe9adf84e43919cb"
-dependencies = [
- "libc",
-]
-
-[[package]]
-name = "matchers"
-version = "0.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8263075bb86c5a1b1427b5ae862e8889656f126e9f77c484496e8b47cf5c5558"
-dependencies = [
- "regex-automata 0.1.10",
-]
-
 [[package]]
 name = "matrixmultiply"
 version = "0.3.9"
@@ -3042,15 +2936,6 @@ dependencies = [
  "libc",
 ]
 
-[[package]]
-name = "memoffset"
-version = "0.7.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5de893c32cde5f383baa4c04c5d6dbdd735cfd4a794b0debdb2bb1b421da5ff4"
-dependencies = [
- "autocfg",
-]
-
 [[package]]
 name = "memoffset"
 version = "0.9.1"
@@ -3128,19 +3013,6 @@ dependencies = [
  "rustc_version 0.1.7",
 ]
 
-[[package]]
-name = "nix"
-version = "0.26.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "598beaf3cc6fdd9a5dfb1630c2800c7acd31df7aaf0f565796fba2b53ca1af1b"
-dependencies = [
- "bitflags 1.3.2",
- "cfg-if",
- "libc",
- "memoffset 0.7.1",
- "pin-utils",
-]
-
 [[package]]
 name = "nix"
 version = "0.29.0"
@@ -3345,16 +3217,6 @@ dependencies = [
  "percent-encoding",
 ]
 
-[[package]]
-name = "nu-ansi-term"
-version = "0.46.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77a8165726e8236064dbb45459242600304b42a5ea24ee2948e18e023bf7ba84"
-dependencies = [
- "overload",
- "winapi",
-]
-
 [[package]]
 name = "num"
 version = "0.4.3"
@@ -3458,35 +3320,6 @@ version = "0.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e25be21376a772d15f97ae789845340a9651d3c4246ff5ebb6a2b35f9c37bd31"
 
-[[package]]
-name = "objc"
-version = "0.2.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "915b1b472bc21c53464d6c8461c9d3af805ba1ef837e1cac254428f4a77177b1"
-dependencies = [
- "malloc_buf",
-]
-
-[[package]]
-name = "objc-foundation"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1add1b659e36c9607c7aab864a76c7a4c2760cd0cd2e120f3fb8b952c7e22bf9"
-dependencies = [
- "block",
- "objc",
- "objc_id",
-]
-
-[[package]]
-name = "objc_id"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c92d4ddb4bd7b50d730c215ff871754d0da6b2178849f8a2a2ab69712d0c073b"
-dependencies = [
- "objc",
-]
-
 [[package]]
 name = "object"
 version = "0.36.7"
@@ -3524,17 +3357,6 @@ dependencies = [
  "vcpkg",
 ]
 
-[[package]]
-name = "opimps"
-version = "0.1.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "68e9faf4b2c7b2387c6d0ff631ebef992a0e7bd0c5e847d2faedf1f49c268d3e"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 1.0.109",
-]
-
 [[package]]
 name = "option-ext"
 version = "0.2.0"
@@ -3557,12 +3379,6 @@ version = "0.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7f222829ae9293e33a9f5e9f440c6760a3d450a64affe1846486b140db81c1f4"
 
-[[package]]
-name = "overload"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b15813163c1d831bf4a13c3610c05c0d03b39feb07f7e09fa234dac9b15aaf39"
-
 [[package]]
 name = "palette"
 version = "0.7.6"
@@ -3596,7 +3412,7 @@ dependencies = [
  "bam",
  "csv",
  "duct",
- "env_logger 0.11.6",
+ "env_logger",
  "flate2",
  "glob",
  "log",
@@ -3614,23 +3430,6 @@ dependencies = [
  "uuid",
 ]
 
-[[package]]
-name = "pandora_lib_bindings"
-version = "0.1.0"
-source = "git+https://git.t0m4.fr/Thomas/pandora_lib_bindings.git#0baaa7c31077d922c873eb47efce37ab4f8a6718"
-dependencies = [
- "anyhow",
- "env_logger 0.10.2",
- "futures",
- "indicatif",
- "log",
- "regex",
- "serde",
- "serde_json",
- "tokio",
- "uuid",
-]
-
 [[package]]
 name = "pandora_lib_blastn"
 version = "0.1.0"
@@ -3638,7 +3437,7 @@ source = "git+https://git.t0m4.fr/Thomas/pandora_lib_blastn.git#4e9ed4b89ab78801
 dependencies = [
  "anyhow",
  "confy",
- "env_logger 0.11.6",
+ "env_logger",
  "log",
  "num-format",
  "serde",
@@ -3679,7 +3478,7 @@ source = "git+https://git.t0m4.fr/Thomas/pandora_lib_pileup.git#9eacd9f3225020bf
 dependencies = [
  "anyhow",
  "average",
- "env_logger 0.11.6",
+ "env_logger",
  "log",
  "noodles-fasta 0.46.0",
  "rayon",
@@ -3696,49 +3495,37 @@ dependencies = [
  "bgzip",
  "blake3",
  "byte-unit",
- "charming",
  "chrono",
  "csv",
  "ctrlc",
  "dashmap",
  "dirs",
  "duct",
- "env_logger 0.11.6",
- "expectrl",
- "features",
- "full",
+ "env_logger",
  "glob",
  "hashbrown 0.15.2",
  "indicatif",
  "itertools 0.14.0",
  "lazy_static",
- "locale_config",
  "log",
- "logtest",
  "noodles-core 0.16.0",
  "noodles-csi 0.43.0",
  "noodles-fasta 0.48.0",
  "noodles-gff 0.43.0",
  "num-format",
  "pandora_lib_assembler",
- "pandora_lib_bindings",
  "pandora_lib_scan",
  "pandora_lib_variants",
  "podders",
- "ptyprocess",
  "rand 0.9.0",
  "rayon",
- "regex",
  "rusqlite",
  "rust-htslib 0.49.0",
  "serde",
  "serde_json",
  "tar",
  "tempfile",
- "test-log",
- "tokio",
  "tracing",
- "tracing-test",
  "uuid",
 ]
 
@@ -3751,7 +3538,7 @@ dependencies = [
  "charming",
  "csv",
  "dashmap",
- "env_logger 0.11.6",
+ "env_logger",
  "indexmap",
  "indicatif",
  "indicatif-log-bridge",
@@ -3780,7 +3567,7 @@ dependencies = [
  "crossbeam-deque",
  "csv",
  "dashmap",
- "env_logger 0.11.6",
+ "env_logger",
  "flate2",
  "hashbrown 0.15.2",
  "indicatif",
@@ -4179,15 +3966,6 @@ dependencies = [
  "syn 1.0.109",
 ]
 
-[[package]]
-name = "ptyprocess"
-version = "0.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7e05aef7befb11a210468a2d77d978dde2c6381a0381e33beb575e91f57fe8cf"
-dependencies = [
- "nix 0.26.4",
-]
-
 [[package]]
 name = "qcms"
 version = "0.3.0"
@@ -4385,17 +4163,8 @@ checksum = "b544ef1b4eac5dc2db33ea63606ae9ffcfac26c1416a2806ae0bf5f56b201191"
 dependencies = [
  "aho-corasick",
  "memchr",
- "regex-automata 0.4.9",
- "regex-syntax 0.8.5",
-]
-
-[[package]]
-name = "regex-automata"
-version = "0.1.10"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132"
-dependencies = [
- "regex-syntax 0.6.29",
+ "regex-automata",
+ "regex-syntax",
 ]
 
 [[package]]
@@ -4406,15 +4175,9 @@ checksum = "809e8dc61f6de73b46c85f4c96486310fe304c434cfa43669d7b40f711150908"
 dependencies = [
  "aho-corasick",
  "memchr",
- "regex-syntax 0.8.5",
+ "regex-syntax",
 ]
 
-[[package]]
-name = "regex-syntax"
-version = "0.6.29"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1"
-
 [[package]]
 name = "regex-syntax"
 version = "0.8.5"
@@ -4945,15 +4708,6 @@ dependencies = [
  "digest",
 ]
 
-[[package]]
-name = "sharded-slab"
-version = "0.1.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f40ca3c46823713e0d4209592e8d6e826aa57e928f09752619fc696c499637f6"
-dependencies = [
- "lazy_static",
-]
-
 [[package]]
 name = "shared_child"
 version = "1.0.1"
@@ -5306,7 +5060,7 @@ dependencies = [
  "fnv",
  "once_cell",
  "plist",
- "regex-syntax 0.8.5",
+ "regex-syntax",
  "serde",
  "serde_derive",
  "serde_json",
@@ -5357,37 +5111,6 @@ dependencies = [
  "winapi",
 ]
 
-[[package]]
-name = "termcolor"
-version = "1.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755"
-dependencies = [
- "winapi-util",
-]
-
-[[package]]
-name = "test-log"
-version = "0.2.16"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3dffced63c2b5c7be278154d76b479f9f9920ed34e7574201407f0b14e2bbb93"
-dependencies = [
- "env_logger 0.11.6",
- "test-log-macros",
- "tracing-subscriber",
-]
-
-[[package]]
-name = "test-log-macros"
-version = "0.2.16"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5999e24eaa32083191ba4e425deb75cdf25efefabe5aaccb7446dd0d4122a3f5"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.95",
-]
-
 [[package]]
 name = "thiserror"
 version = "1.0.69"
@@ -5428,16 +5151,6 @@ dependencies = [
  "syn 2.0.95",
 ]
 
-[[package]]
-name = "thread_local"
-version = "1.1.8"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8b9ef9bad013ada3808854ceac7b46812a6465ba368859a37e2100283d2d719c"
-dependencies = [
- "cfg-if",
- "once_cell",
-]
-
 [[package]]
 name = "tiff"
 version = "0.9.1"
@@ -5633,57 +5346,6 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e672c95779cf947c5311f83787af4fa8fffd12fb27e4993211a84bdfd9610f9c"
 dependencies = [
  "once_cell",
- "valuable",
-]
-
-[[package]]
-name = "tracing-log"
-version = "0.2.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ee855f1f400bd0e5c02d150ae5de3840039a3f54b025156404e34c23c03f47c3"
-dependencies = [
- "log",
- "once_cell",
- "tracing-core",
-]
-
-[[package]]
-name = "tracing-subscriber"
-version = "0.3.19"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e8189decb5ac0fa7bc8b96b7cb9b2701d60d48805aca84a238004d665fcc4008"
-dependencies = [
- "matchers",
- "nu-ansi-term",
- "once_cell",
- "regex",
- "sharded-slab",
- "smallvec",
- "thread_local",
- "tracing",
- "tracing-core",
- "tracing-log",
-]
-
-[[package]]
-name = "tracing-test"
-version = "0.2.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "557b891436fe0d5e0e363427fc7f217abf9ccd510d5136549847bdcbcd011d68"
-dependencies = [
- "tracing-core",
- "tracing-subscriber",
- "tracing-test-macro",
-]
-
-[[package]]
-name = "tracing-test-macro"
-version = "0.2.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "04659ddb06c87d233c566112c1c9c5b9e98256d9af50ec3bc9c8327f873a7568"
-dependencies = [
- "quote",
- "syn 2.0.95",
 ]
 
 [[package]]
@@ -6277,18 +5939,6 @@ dependencies = [
  "which 6.0.3",
 ]
 
-[[package]]
-name = "valuable"
-version = "0.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "830b7e5d4d90034032940e4ace0d9a9a057e7a45cd94e6c007832e39edb82f6d"
-
-[[package]]
-name = "value-bag"
-version = "1.10.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3ef4c4aa54d5d05a279399bfa921ec387b7aba77caf7a682ae8d86785b8fdad2"
-
 [[package]]
 name = "vcpkg"
 version = "0.2.15"
@@ -6510,15 +6160,6 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
 
-[[package]]
-name = "windows"
-version = "0.44.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9e745dab35a0c4c77aa3ce42d595e13d2003d6902d6b08c9ef5fc326d08da12b"
-dependencies = [
- "windows-targets 0.42.2",
-]
-
 [[package]]
 name = "windows-core"
 version = "0.52.0"
@@ -6555,21 +6196,6 @@ dependencies = [
  "windows-targets 0.52.6",
 ]
 
-[[package]]
-name = "windows-targets"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071"
-dependencies = [
- "windows_aarch64_gnullvm 0.42.2",
- "windows_aarch64_msvc 0.42.2",
- "windows_i686_gnu 0.42.2",
- "windows_i686_msvc 0.42.2",
- "windows_x86_64_gnu 0.42.2",
- "windows_x86_64_gnullvm 0.42.2",
- "windows_x86_64_msvc 0.42.2",
-]
-
 [[package]]
 name = "windows-targets"
 version = "0.48.5"
@@ -6601,12 +6227,6 @@ dependencies = [
  "windows_x86_64_msvc 0.52.6",
 ]
 
-[[package]]
-name = "windows_aarch64_gnullvm"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8"
-
 [[package]]
 name = "windows_aarch64_gnullvm"
 version = "0.48.5"
@@ -6619,12 +6239,6 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
 
-[[package]]
-name = "windows_aarch64_msvc"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43"
-
 [[package]]
 name = "windows_aarch64_msvc"
 version = "0.48.5"
@@ -6637,12 +6251,6 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
 
-[[package]]
-name = "windows_i686_gnu"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f"
-
 [[package]]
 name = "windows_i686_gnu"
 version = "0.48.5"
@@ -6661,12 +6269,6 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
 
-[[package]]
-name = "windows_i686_msvc"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060"
-
 [[package]]
 name = "windows_i686_msvc"
 version = "0.48.5"
@@ -6679,12 +6281,6 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
 
-[[package]]
-name = "windows_x86_64_gnu"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36"
-
 [[package]]
 name = "windows_x86_64_gnu"
 version = "0.48.5"
@@ -6697,12 +6293,6 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
 
-[[package]]
-name = "windows_x86_64_gnullvm"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3"
-
 [[package]]
 name = "windows_x86_64_gnullvm"
 version = "0.48.5"
@@ -6715,12 +6305,6 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
 
-[[package]]
-name = "windows_x86_64_msvc"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0"
-
 [[package]]
 name = "windows_x86_64_msvc"
 version = "0.48.5"

Cargo.toml

@@ -8,25 +8,17 @@ log = "^0.4.22"
 env_logger = "^0.11.3"
 anyhow = "1.0.86"
 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" }
 pandora_lib_assembler = { git = "https://git.t0m4.fr/Thomas/pandora_lib_assembler.git" }
-regex = "1.10.5"
 chrono = { version = "0.4.38", features = ["serde"] }
 csv = "1.3.0"
 serde = { version = "1.0.204", features = ["derive"] }
 serde_json = "1.0"
-tracing-test = "0.2.5"
 tracing = "0.1.40"
-logtest = "2.0.0"
-test-log = "0.2.16"
 noodles-csi = "0.43.0"
 num-format = "0.4.4"
-locale_config = "0.3.0"
 byte-unit = "5.1.4"
-expectrl = "0.7.1"
-ptyprocess = "0.4.1"
 duct = "0.13.7"
 uuid = { version = "1.13.1", features = ["v4"] }
 rayon = "1.10.0"
@@ -34,9 +26,6 @@ hashbrown = { version = "0.15.0", features = ["rayon"] }
 ctrlc = "3.4.4"
 lazy_static = "1.5.0"
 indicatif = "0.17.8"
-tokio = "1.41.1"
-features = "0.10.0"
-full = "0.3.0"
 rust-htslib = "0.49.0"
 podders = "0.1.4"
 arrow = "54.0.0"
@@ -46,7 +35,6 @@ dashmap = { version = "6.1.0", features = ["rayon", "serde"] }
 noodles-fasta = "0.48.0"
 noodles-core = "0.16.0"
 blake3 = "1.5.5"
-charming = { version = "0.4.0", features = ["ssr"] }
 rusqlite = { version = "0.32.1", features = ["chrono", "serde_json"] }
 dirs = "6.0.0"
 noodles-gff = "0.43.0"

src/collection/bam.rs

@@ -9,7 +9,7 @@ use chrono::{DateTime, Utc};
 use dashmap::DashMap;
 use glob::glob;
 use log::{debug, info, warn};
-use rand::{thread_rng, Rng};
+use rand::{rng, Rng};
 use rayon::prelude::*;
 use rust_htslib::bam::{ext::BamRecordExtensions, record::Cigar, Read};
 use serde::{Deserialize, Serialize};
@@ -519,12 +519,12 @@ pub fn counts_ins_at(
 }
 
 pub fn sample_random_positions(chromosomes: &Vec<(String, u64)>, n: usize) -> Vec<(String, u64)> {
-    let mut rng = thread_rng();
+    let mut rng = rng();
     let total_length: u64 = chromosomes.iter().map(|(_, length)| length).sum();
 
     (0..n)
         .map(|_| {
-            let random_position = rng.gen_range(0..total_length);
+            let random_position = rng.random_range(0..total_length);
             let mut cumulative_length = 0;
 
             for (chr, length) in chromosomes {