diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0b355fb..b4792bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## 1.2.0
 
 - Fix: Handle BAM records with empty SEQ fields (`*` in SAM format) in `base-depth`. Previously this would cause an out-of-bounds error. Now these reads still count toward depth, and their bases are counted as `N`. ([#92](https://github.com/sstadick/perbase/pull/92) by @ghuls)
+- Chore: Update deps and fixup lints
 
 ## 1.1.0
 
diff --git a/Cargo.lock b/Cargo.lock
index 9f1f1a2..29481da 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -3,16 +3,16 @@
 version = 4
 
 [[package]]
-name = "adler"
-version = "1.0.2"
+name = "adler2"
+version = "2.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
+checksum = "320119579fcad9c21884f5c4861d16174d0e06250625266f50fe6898340abefa"
 
 [[package]]
 name = "aho-corasick"
-version = "1.1.2"
+version = "1.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0"
+checksum = "ddd31a130427c27518df266943a5308ed92d4b226cc639f5a8f1002816174301"
 dependencies = [
  "memchr",
 ]
@@ -23,14 +23,64 @@ version = "0.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d52a9bb7ec0cf484c551830a7ce27bd20d67eac647e1befb56b0be4ee39a55d2"
 dependencies = [
- "winapi 0.3.9",
+ "winapi",
+]
+
+[[package]]
+name = "anstream"
+version = "0.6.21"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "43d5b281e737544384e969a5ccad3f1cdd24b48086a0fc1b2a5262a26b8f4f4a"
+dependencies = [
+ "anstyle",
+ "anstyle-parse",
+ "anstyle-query",
+ "anstyle-wincon",
+ "colorchoice",
+ "is_terminal_polyfill",
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle"
+version = "1.0.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5192cca8006f1fd4f7237516f40fa183bb07f8fbdfedaa0036de5ea9b0b45e78"
+
+[[package]]
+name = "anstyle-parse"
+version = "0.2.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4e7644824f0aa2c7b9384579234ef10eb7efb6a0deb83f9630a49594dd9c15c2"
+dependencies = [
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle-query"
+version = "1.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "40c48f72fd53cd289104fc64099abca73db4166ad86ea0b4341abe65af83dadc"
+dependencies = [
+ "windows-sys",
+]
+
+[[package]]
+name = "anstyle-wincon"
+version = "3.0.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "291e6a250ff86cd4a820112fb8898808a366d8f9f58ce16d1f538353ad55747d"
+dependencies = [
+ "anstyle",
+ "once_cell_polyfill",
+ "windows-sys",
 ]
 
 [[package]]
 name = "anyhow"
-version = "1.0.75"
+version = "1.0.100"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6"
+checksum = "a23eb6b1614318a8071c9b2521f36b424b2c83db5eb3a0fead4a6c0809af6e61"
 
 [[package]]
 name = "approx"
@@ -49,20 +99,40 @@ checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
 dependencies = [
  "hermit-abi 0.1.19",
  "libc",
- "winapi 0.3.9",
+ "winapi",
 ]
 
 [[package]]
 name = "autocfg"
-version = "1.1.0"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
+checksum = "c08606f8c3cbf4ce6ec8e28fb0014a2c086708fe954eaa885384a6165172e7e8"
+
+[[package]]
+name = "bindgen"
+version = "0.69.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "271383c67ccabffb7381723dea0672a673f292304fcb45c01cc648c7a8d58088"
+dependencies = [
+ "bitflags 2.10.0",
+ "cexpr",
+ "clang-sys",
+ "itertools 0.12.1",
+ "lazy_static",
+ "lazycell",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "regex",
+ "rustc-hash",
+ "shlex",
+ "syn 2.0.111",
+]
 
 [[package]]
 name = "bio"
-version = "0.41.0"
+version = "3.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4a69423e30444738eccc5e54eccee75779dd3f15ecc0469b95d8529d4b6b7586"
+checksum = "2169c40f17068bcf0563e5060ed6ccab694f68068133055f6e96bcdf987b3f32"
 dependencies = [
  "anyhow",
  "approx",
@@ -72,12 +142,13 @@ dependencies = [
  "bytecount",
  "csv",
  "custom_derive",
+ "derefable",
+ "editdistancek",
  "enum-map",
  "fxhash",
  "getset",
- "itertools",
+ "itertools 0.12.1",
  "itertools-num",
- "lazy_static",
  "multimap",
  "ndarray",
  "newtype_derive",
@@ -85,45 +156,44 @@ dependencies = [
  "num-traits",
  "ordered-float",
  "petgraph",
- "rand",
  "regex",
  "serde",
  "serde_derive",
  "statrs",
  "strum 0.23.0",
- "strum_macros 0.23.1",
- "thiserror",
+ "strum_macros 0.26.4",
+ "thiserror 2.0.17",
  "triple_accel",
  "vec_map",
 ]
 
 [[package]]
 name = "bio-types"
-version = "1.0.1"
+version = "1.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9d45749b87f21808051025e9bf714d14ff4627f9d8ca967eade6946ea769aa4a"
+checksum = "f4dcf54f8b7f51450207d54780bab09c05f30b8b0caa991545082842e466ad7e"
 dependencies = [
- "derive-new",
+ "derive-new 0.6.0",
  "lazy_static",
  "regex",
- "strum_macros 0.25.2",
- "thiserror",
+ "strum_macros 0.26.4",
+ "thiserror 1.0.69",
 ]
 
 [[package]]
 name = "bit-set"
-version = "0.5.3"
+version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1"
+checksum = "08807e080ed7f9d5433fa9b275196cfc35414f66a0c79d864dc51a0d825231a3"
 dependencies = [
  "bit-vec",
 ]
 
 [[package]]
 name = "bit-vec"
-version = "0.6.3"
+version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
+checksum = "5e764a1d40d510daf35e07be9eb06e75770908c27d411ee6c92109c9840eaaf7"
 
 [[package]]
 name = "bitflags"
@@ -133,15 +203,15 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
 
 [[package]]
 name = "bitflags"
-version = "2.4.0"
+version = "2.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b4682ae6287fcf752ecaabbfcc7b6f9b72aa33933dc23a554d853aea8eea8635"
+checksum = "812e12b5285cc515a9c72a5c1d3b6d46a19dac5acfef5265968c166106e31dd3"
 
 [[package]]
 name = "bstr"
-version = "1.7.0"
+version = "1.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c79ad7fb2dd38f3dabd76b09c6a5a20c038fc0213ef1e9afd30eb777f120f019"
+checksum = "63044e1ae8e69f3b5a92c736ca6269b8d12fa7efe39bf34ddb06d102cf0e2cab"
 dependencies = [
  "memchr",
  "regex-automata",
@@ -150,9 +220,9 @@ dependencies = [
 
 [[package]]
 name = "bumpalo"
-version = "3.14.0"
+version = "3.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec"
+checksum = "46c5e41b57b8bba42a04676d81cb89e9ee8e859a1a66f80a5a72e1cb76b34d43"
 
 [[package]]
 name = "bv"
@@ -166,9 +236,9 @@ dependencies = [
 
 [[package]]
 name = "bytecount"
-version = "0.6.4"
+version = "0.6.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ad152d03a2c813c80bb94fedbf3a3f02b28f793e39e7c214c8a0bcc196343de7"
+checksum = "175812e0be2bccb6abe50bb8d566126198344f707e304f45c648fd8f2cc0365e"
 
 [[package]]
 name = "byteorder"
@@ -178,36 +248,47 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bytes"
-version = "1.5.0"
+version = "1.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223"
+checksum = "b35204fbdc0b3f4446b89fc1ac2cf84a8a68971995d0bf2e925ec7cd960f9cb3"
 
 [[package]]
-name = "bzip2-sys"
-version = "0.1.11+1.0.8"
+name = "cc"
+version = "1.2.49"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc"
+checksum = "90583009037521a116abf44494efecd645ba48b6622457080f080b85544e2215"
 dependencies = [
- "cc",
+ "find-msvc-tools",
+ "jobserver",
  "libc",
- "pkg-config",
+ "shlex",
 ]
 
 [[package]]
-name = "cc"
-version = "1.0.83"
+name = "cexpr"
+version = "0.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0"
+checksum = "6fac387a98bb7c37292057cffc56d62ecb629900026402633ae9160df93a8766"
 dependencies = [
- "jobserver",
- "libc",
+ "nom",
 ]
 
 [[package]]
 name = "cfg-if"
-version = "1.0.0"
+version = "1.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
+checksum = "9330f8b2ff13f34540b44e946ef35111825727b38d33286ef986142615121801"
+
+[[package]]
+name = "clang-sys"
+version = "1.8.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b023947811758c97c59bf9d1c188fd619ad4718dcaa767947df1cadb14f39f4"
+dependencies = [
+ "glob",
+ "libc",
+ "libloading",
+]
 
 [[package]]
 name = "clap"
@@ -226,41 +307,45 @@ dependencies = [
 
 [[package]]
 name = "cmake"
-version = "0.1.50"
+version = "0.1.54"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130"
+checksum = "e7caa3f9de89ddbe2c607f4101924c5abec803763ae9534e4f4d7d8f84aa81f0"
 dependencies = [
  "cc",
 ]
 
+[[package]]
+name = "colorchoice"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b05b61dc5112cbb17e4b6cd61790d9845d13888356391624cbe7e41efeac1e75"
+
 [[package]]
 name = "core_affinity"
-version = "0.5.10"
+version = "0.8.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f8a03115cc34fb0d7c321dd154a3914b3ca082ccc5c11d91bf7117dbbe7171f"
+checksum = "a034b3a7b624016c6e13f5df875747cc25f884156aad2abd12b6c46797971342"
 dependencies = [
- "kernel32-sys",
  "libc",
  "num_cpus",
- "winapi 0.2.8",
+ "winapi",
 ]
 
 [[package]]
 name = "crc32fast"
-version = "1.3.2"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d"
+checksum = "9481c1c90cbf2ac953f07c8d4a58aa3945c425b7185c9154d67a65e4230da511"
 dependencies = [
  "cfg-if",
 ]
 
 [[package]]
 name = "crossbeam"
-version = "0.8.2"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2801af0d36612ae591caa9568261fddce32ce6e08a7275ea334a06a4ad021a2c"
+checksum = "1137cd7e7fc0fb5d3c5a8678be38ec56e819125d8d7907411fe24ccb943faca8"
 dependencies = [
- "cfg-if",
  "crossbeam-channel",
  "crossbeam-deque",
  "crossbeam-epoch",
@@ -270,115 +355,129 @@ dependencies = [
 
 [[package]]
 name = "crossbeam-channel"
-version = "0.5.8"
+version = "0.5.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a33c2bf77f2df06183c3aa30d1e96c0695a313d4f9c453cc3762a6db39f99200"
+checksum = "82b8f8f868b36967f9606790d1903570de9ceaf870a7bf9fbbd3016d636a2cb2"
 dependencies = [
- "cfg-if",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-deque"
-version = "0.8.3"
+version = "0.8.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef"
+checksum = "9dd111b7b7f7d55b72c0a6ae361660ee5853c9af73f70c3c2ef6858b950e2e51"
 dependencies = [
- "cfg-if",
  "crossbeam-epoch",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-epoch"
-version = "0.9.15"
+version = "0.9.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7"
+checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e"
 dependencies = [
- "autocfg",
- "cfg-if",
  "crossbeam-utils",
- "memoffset",
- "scopeguard",
 ]
 
 [[package]]
 name = "crossbeam-queue"
-version = "0.3.8"
+version = "0.3.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d1cfb3ea8a53f37c40dea2c7bedcbd88bdfae54f5e2175d6ecaff1c988353add"
+checksum = "0f58bbc28f91df819d0aa2a2c00cd19754769c2fad90579b3592b1c9ba7a3115"
 dependencies = [
- "cfg-if",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-utils"
-version = "0.8.16"
+version = "0.8.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294"
-dependencies = [
- "cfg-if",
-]
+checksum = "d0a5c400df2834b80a4c3327b3aad3a4c4cd4de0629063962b03235697506a28"
 
 [[package]]
 name = "csv"
-version = "1.3.0"
+version = "1.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac574ff4d437a7b5ad237ef331c17ccca63c46479e5b5453eb8e10bb99a759fe"
+checksum = "52cd9d68cf7efc6ddfaaee42e7288d3a99d613d4b50f76ce9827ae0c6e14f938"
 dependencies = [
  "csv-core",
  "itoa",
  "ryu",
- "serde",
+ "serde_core",
 ]
 
 [[package]]
 name = "csv-core"
-version = "0.1.11"
+version = "0.1.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5efa2b3d7902f4b634a20cae3c9c4e6209dc4779feb6863329607560143efa70"
+checksum = "704a3c26996a80471189265814dbc2c257598b96b8a7feae2d31ace646bb9782"
 dependencies = [
  "memchr",
 ]
 
 [[package]]
-name = "curl-sys"
-version = "0.4.67+curl-8.3.0"
+name = "custom_derive"
+version = "0.1.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3cc35d066510b197a0f72de863736641539957628c8a42e70e27c66849e77c34"
+checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
+
+[[package]]
+name = "derefable"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e519abf1289075763071c981958e89948b079fc54962617a0e6413d9ce44cbe7"
 dependencies = [
- "cc",
- "libc",
- "libz-sys",
- "openssl-sys",
- "pkg-config",
- "vcpkg",
- "windows-sys",
+ "proc-macro2 0.4.30",
+ "quote 0.6.13",
+ "syn 0.15.44",
 ]
 
 [[package]]
-name = "custom_derive"
-version = "0.1.7"
+name = "derive-new"
+version = "0.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
+checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
 
 [[package]]
 name = "derive-new"
-version = "0.5.9"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535"
+checksum = "2cdc8d50f426189eef89dac62fabfa0abb27d5cc008f25bf4156a0203325becc"
 dependencies = [
- "proc-macro2",
- "quote",
- "syn 1.0.109",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
+
+[[package]]
+name = "displaydoc"
+version = "0.2.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "97369cbbc041bc366949bc74d34658d6cda5621039731c6310521892a3a20ae0"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
 ]
 
+[[package]]
+name = "editdistancek"
+version = "1.0.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3e02df23d5b1c6f9e69fa603b890378123b93073df998a21e6e33b9db0a32613"
+
 [[package]]
 name = "either"
-version = "1.9.0"
+version = "1.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07"
+checksum = "48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719"
 
 [[package]]
 name = "enum-map"
@@ -395,35 +494,45 @@ version = "0.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "84278eae0af6e34ff6c1db44c11634a694aafac559ff3080e4db4e4ac35907aa"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "syn 1.0.109",
 ]
 
 [[package]]
-name = "env_logger"
-version = "0.9.3"
+name = "env_filter"
+version = "0.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a12e6657c4c97ebab115a42dcee77225f7f482cdd841cf7088c657a42e9e00e7"
+checksum = "1bf3c259d255ca70051b30e2e95b5446cdb8949ac4cd22c0d7fd634d89f568e2"
 dependencies = [
- "atty",
- "humantime",
  "log",
  "regex",
- "termcolor",
+]
+
+[[package]]
+name = "env_logger"
+version = "0.11.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "13c863f0904021b108aa8b2f55046443e6b1ebde8fd4a15c399893aae4fa069f"
+dependencies = [
+ "anstream",
+ "anstyle",
+ "env_filter",
+ "jiff",
+ "log",
 ]
 
 [[package]]
 name = "equivalent"
-version = "1.0.1"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
+checksum = "877a4ace8713b0bcf2a4e7eec82529c029f1d0619886d18145fea96c3ffe5c0f"
 
 [[package]]
 name = "errno"
-version = "0.3.5"
+version = "0.3.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac3e13f66a2f95e32a39eaa81f6b95d42878ca0e1db0c7543723dfe12557e860"
+checksum = "39cab71617ae0d63f51a36d69f866391735b51691dbda63cf6f96d042b63efeb"
 dependencies = [
  "libc",
  "windows-sys",
@@ -431,9 +540,9 @@ dependencies = [
 
 [[package]]
 name = "fastrand"
-version = "2.0.1"
+version = "2.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "25cbce373ec4653f1a01a31e8a5e5ec0c622dc27ff9c4e6606eefef5cbbed4a5"
+checksum = "37909eebbb50d72f9059c3b6d82c0463f2ff062c9e95845c43a6c9c0355411be"
 
 [[package]]
 name = "feature-probe"
@@ -441,6 +550,12 @@ version = "0.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "835a3dc7d1ec9e75e2b5fb4ba75396837112d2060b03f7d43bc1897c7f7211da"
 
+[[package]]
+name = "find-msvc-tools"
+version = "0.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3a3076410a55c90011c298b04d0cfa770b00fa04e1e3c97d3f6c9de105a03844"
+
 [[package]]
 name = "fixedbitset"
 version = "0.4.2"
@@ -449,25 +564,24 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
 [[package]]
 name = "flate2"
-version = "1.0.27"
+version = "1.1.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c6c98ee8095e9d1dcbf2fcc6d95acccb90d1c81db1e44725c6a984b1dbdfb010"
+checksum = "bfe33edd8e85a12a67454e37f8c75e730830d83e313556ab9ebf9ee7fbeb3bfb"
 dependencies = [
  "crc32fast",
- "libz-sys",
+ "libz-ng-sys",
  "miniz_oxide",
 ]
 
 [[package]]
 name = "flume"
-version = "0.10.14"
+version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1657b4441c3403d9f7b3409e47575237dac27b1b5726df654a6ecbf92f0f7577"
+checksum = "da0e4dd2a88388a1f4ccc7c9ce104604dab68d9f408dc34cd45823d5a9069095"
 dependencies = [
  "futures-core",
  "futures-sink",
  "nanorand",
- "pin-project",
  "spin",
 ]
 
@@ -479,9 +593,9 @@ checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
 
 [[package]]
 name = "form_urlencoded"
-version = "1.2.0"
+version = "1.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652"
+checksum = "cb4cb245038516f5f85277875cdaa4f7d2c9a0fa0468de06ed190163b1581fcf"
 dependencies = [
  "percent-encoding",
 ]
@@ -497,15 +611,52 @@ dependencies = [
 
 [[package]]
 name = "futures-core"
-version = "0.3.28"
+version = "0.3.31"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "05f29059c0c2090612e8d742178b0580d2dc940c837851ad723096f87af6663e"
+
+[[package]]
+name = "futures-macro"
+version = "0.3.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4bca583b7e26f571124fe5b7561d49cb2868d79116cfa0eefce955557c6fee8c"
+checksum = "162ee34ebcb7c64a8abebc059ce0fee27c2262618d7b60ed8faf72fef13c3650"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
 
 [[package]]
 name = "futures-sink"
-version = "0.3.28"
+version = "0.3.31"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e575fab7d1e0dcb8d0c7bcf9a63ee213816ab51902e6d244a95819acacf1d4f7"
+
+[[package]]
+name = "futures-task"
+version = "0.3.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f43be4fe21a13b9781a69afa4985b0f6ee0e1afab2c6f454a8cf30e2b2237b6e"
+checksum = "f90f7dce0722e95104fcb095585910c0977252f286e354b5e3bd38902cd99988"
+
+[[package]]
+name = "futures-timer"
+version = "3.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f288b0a4f20f9a56b5d1da57e2227c661b7b16168e2f72365f57b63326e29b24"
+
+[[package]]
+name = "futures-util"
+version = "0.3.31"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9fa08315bb612088cc391249efdc3bc77536f16c91f6cf495e6fbe85b20a4a81"
+dependencies = [
+ "futures-core",
+ "futures-macro",
+ "futures-task",
+ "pin-project-lite",
+ "pin-utils",
+ "slab",
+]
 
 [[package]]
 name = "fxhash"
@@ -518,9 +669,9 @@ dependencies = [
 
 [[package]]
 name = "getrandom"
-version = "0.2.10"
+version = "0.2.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427"
+checksum = "335ff9f135e4384c8150d6f27c6daed433577f86b4750418338c01a1a2528592"
 dependencies = [
  "cfg-if",
  "js-sys",
@@ -529,58 +680,68 @@ dependencies = [
  "wasm-bindgen",
 ]
 
+[[package]]
+name = "getrandom"
+version = "0.3.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "899def5c37c4fd7b2664648c28120ecec138e4d395b459e5ca34f9cce2dd77fd"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "r-efi",
+ "wasip2",
+]
+
 [[package]]
 name = "getset"
-version = "0.1.2"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e45727250e75cc04ff2846a66397da8ef2b3db8e40e0cef4df67950a07621eb9"
+checksum = "9cf0fc11e47561d47397154977bc219f4cf809b2974facc3ccb3b89e2436f912"
 dependencies = [
- "proc-macro-error",
- "proc-macro2",
- "quote",
- "syn 1.0.109",
+ "proc-macro-error2",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
 ]
 
 [[package]]
 name = "glob"
-version = "0.3.1"
+version = "0.3.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
+checksum = "0cc23270f6e1808e30a928bdc84dea0b9b4136a8bc82338574f23baf47bbd280"
 
 [[package]]
 name = "globset"
-version = "0.4.13"
+version = "0.4.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "759c97c1e17c55525b57192c06a267cda0ac5210b222d6b82189a2338fa1c13d"
+checksum = "52dfc19153a48bde0cbd630453615c8151bce3a5adfac7a0aebfbf0a1e1f57e3"
 dependencies = [
  "aho-corasick",
  "bstr",
- "fnv",
  "log",
- "regex",
+ "regex-automata",
+ "regex-syntax",
 ]
 
 [[package]]
 name = "grep-cli"
-version = "0.1.9"
+version = "0.1.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8fe4bdbf4300c8b039f5d7eec7fbc6760d2c85bb15ac7499c4d235667f6d747a"
+checksum = "cf32d263c5d5cc2a23ce587097f5ddafdb188492ba2e6fb638eaccdc22453631"
 dependencies = [
  "bstr",
  "globset",
- "lazy_static",
+ "libc",
  "log",
- "regex",
- "same-file",
  "termcolor",
  "winapi-util",
 ]
 
 [[package]]
 name = "gzp"
-version = "0.10.1"
+version = "2.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bcaa63633f99fe42694dbc0004cdc2ba160d9a303f0d08d2e50380a500a19cf3"
+checksum = "7abe9930717197e0ea50d8c8a1106a38b5bee0536ed4cbf4b93ba1a953f97d04"
 dependencies = [
  "byteorder",
  "bytes",
@@ -588,16 +749,17 @@ dependencies = [
  "flate2",
  "flume",
  "libdeflater",
- "libz-sys",
+ "libz-ng-sys",
+ "log",
  "num_cpus",
- "thiserror",
+ "thiserror 2.0.17",
 ]
 
 [[package]]
 name = "hashbrown"
-version = "0.14.1"
+version = "0.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7dfda62a12f55daeae5015f81b0baea145391cb4520f86c248fc615d72640d12"
+checksum = "841d1cc9bed7f9236f321df977030373f4a4163ae1a7dbfe1a51a2c1a51d9100"
 
 [[package]]
 name = "heck"
@@ -608,12 +770,6 @@ dependencies = [
  "unicode-segmentation",
 ]
 
-[[package]]
-name = "heck"
-version = "0.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
-
 [[package]]
 name = "heck"
 version = "0.5.0"
@@ -631,40 +787,124 @@ dependencies = [
 
 [[package]]
 name = "hermit-abi"
-version = "0.3.3"
+version = "0.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d77f7ec81a6d05a3abb01ab6eb7590f6083d08449fe5a1c8b1e620283546ccb7"
+checksum = "fc0fef456e4baa96da950455cd02c081ca953b141298e41db3fc7e36b1da849c"
 
 [[package]]
 name = "hts-sys"
-version = "2.1.1"
+version = "2.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "deebfb779c734d542e7f14c298597914b9b5425e4089aef482eacb5cab941915"
+checksum = "e38d7f1c121cd22aa214cb4dadd4277dc5447391eac518b899b29ba6356fbbb2"
 dependencies = [
- "bzip2-sys",
+ "bindgen",
  "cc",
- "curl-sys",
  "fs-utils",
  "glob",
+ "libdeflate-sys",
  "libz-sys",
- "lzma-sys",
- "openssl-sys",
 ]
 
 [[package]]
-name = "humantime"
-version = "2.1.0"
+name = "icu_collections"
+version = "2.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4"
+checksum = "4c6b649701667bbe825c3b7e6388cb521c23d88644678e83c0c4d0a621a34b43"
+dependencies = [
+ "displaydoc",
+ "potential_utf",
+ "yoke",
+ "zerofrom",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_locale_core"
+version = "2.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "edba7861004dd3714265b4db54a3c390e880ab658fec5f7db895fae2046b5bb6"
+dependencies = [
+ "displaydoc",
+ "litemap",
+ "tinystr",
+ "writeable",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_normalizer"
+version = "2.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5f6c8828b67bf8908d82127b2054ea1b4427ff0230ee9141c54251934ab1b599"
+dependencies = [
+ "icu_collections",
+ "icu_normalizer_data",
+ "icu_properties",
+ "icu_provider",
+ "smallvec",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_normalizer_data"
+version = "2.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7aedcccd01fc5fe81e6b489c15b247b8b0690feb23304303a9e560f37efc560a"
+
+[[package]]
+name = "icu_properties"
+version = "2.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "020bfc02fe870ec3a66d93e677ccca0562506e5872c650f893269e08615d74ec"
+dependencies = [
+ "icu_collections",
+ "icu_locale_core",
+ "icu_properties_data",
+ "icu_provider",
+ "zerotrie",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_properties_data"
+version = "2.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "616c294cf8d725c6afcd8f55abc17c56464ef6211f9ed59cccffe534129c77af"
+
+[[package]]
+name = "icu_provider"
+version = "2.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "85962cf0ce02e1e0a629cc34e7ca3e373ce20dda4c4d7294bbd0bf1fdb59e614"
+dependencies = [
+ "displaydoc",
+ "icu_locale_core",
+ "writeable",
+ "yoke",
+ "zerofrom",
+ "zerotrie",
+ "zerovec",
+]
 
 [[package]]
 name = "idna"
-version = "0.4.0"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3b0875f23caa03898994f6ddc501886a45c7d3d62d04d2d90788d47be1b1e4de"
+dependencies = [
+ "idna_adapter",
+ "smallvec",
+ "utf8_iter",
+]
+
+[[package]]
+name = "idna_adapter"
+version = "1.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7d20d6b07bfbc108882d88ed8e37d39636dcc260e15e30c45e6ba089610b917c"
+checksum = "3acae9609540aa318d1bc588455225fb2085b9ed0c4f6bd0d9d5bcd86f1a0344"
 dependencies = [
- "unicode-bidi",
- "unicode-normalization",
+ "icu_normalizer",
+ "icu_properties",
 ]
 
 [[package]]
@@ -675,19 +915,34 @@ checksum = "9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c"
 
 [[package]]
 name = "indexmap"
-version = "2.0.2"
+version = "2.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8adf3ddd720272c6ea8bf59463c04e0f93d0bbf7c5439b691bca2987e0270897"
+checksum = "0ad4bb2b565bca0645f4d68c5c9af97fba094e9791da685bf83cb5f3ce74acf2"
 dependencies = [
  "equivalent",
  "hashbrown",
 ]
 
+[[package]]
+name = "is_terminal_polyfill"
+version = "1.70.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a6cb138bb79a146c1bd460005623e142ef0181e3d0219cb493e02f7d08a35695"
+
+[[package]]
+name = "itertools"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569"
+dependencies = [
+ "either",
+]
+
 [[package]]
 name = "itertools"
-version = "0.10.5"
+version = "0.14.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473"
+checksum = "2b192c782037fadd9cfa75548310488aabdbf3d2da73885b31bd0abd03351285"
 dependencies = [
  "either",
 ]
@@ -703,79 +958,121 @@ dependencies = [
 
 [[package]]
 name = "itoa"
-version = "1.0.9"
+version = "1.0.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "af150ab688ff2122fcef229be89cb50dd66af9e01a4ff320cc137eecc9bacc38"
+checksum = "4a5f13b858c8d314ee3e8f639011f7ccefe71f97f96e50151fb991f267928e2c"
+
+[[package]]
+name = "jiff"
+version = "0.2.16"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "49cce2b81f2098e7e3efc35bc2e0a6b7abec9d34128283d7a26fa8f32a6dbb35"
+dependencies = [
+ "jiff-static",
+ "log",
+ "portable-atomic",
+ "portable-atomic-util",
+ "serde_core",
+]
+
+[[package]]
+name = "jiff-static"
+version = "0.2.16"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "980af8b43c3ad5d8d349ace167ec8170839f753a42d233ba19e08afe1850fa69"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
 
 [[package]]
 name = "jobserver"
-version = "0.1.27"
+version = "0.1.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8c37f63953c4c63420ed5fd3d6d398c719489b9f872b9fa683262f8edd363c7d"
+checksum = "9afb3de4395d6b3e67a780b6de64b51c978ecf11cb9a462c66be7d4ca9039d33"
 dependencies = [
+ "getrandom 0.3.4",
  "libc",
 ]
 
 [[package]]
 name = "js-sys"
-version = "0.3.64"
+version = "0.3.83"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c5f195fe497f702db0f318b07fdd68edb16955aed830df8363d837542f8f935a"
+checksum = "464a3709c7f55f1f721e5389aa6ea4e3bc6aba669353300af094b29ffbdde1d8"
 dependencies = [
+ "once_cell",
  "wasm-bindgen",
 ]
 
 [[package]]
-name = "kernel32-sys"
-version = "0.2.2"
+name = "lazy_static"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7507624b29483431c0ba2d82aece8ca6cdba9382bff4ddd0f7490560c056098d"
-dependencies = [
- "winapi 0.2.8",
- "winapi-build",
-]
+checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
-name = "lazy_static"
-version = "1.4.0"
+name = "lazycell"
+version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55"
 
 [[package]]
 name = "libc"
-version = "0.2.149"
+version = "0.2.178"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a08173bc88b7955d1b3145aa561539096c421ac8debde8cbc3612ec635fee29b"
+checksum = "37c93d8daa9d8a012fd8ab92f088405fb202ea0b6ab73ee2482ae66af4f42091"
 
 [[package]]
 name = "libdeflate-sys"
-version = "0.7.5"
+version = "1.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4cceaf6e335d658ec0602685bfe50d0f35248d6d8848b194058bfda37a9eb728"
+checksum = "23bd6304ebf75390d8a99b88bdf2a266f62647838140cb64af8e6702f6e3fddc"
 dependencies = [
  "cc",
 ]
 
 [[package]]
 name = "libdeflater"
-version = "0.7.5"
+version = "1.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "15f0c115fd181333eb7a82cf42e2ce2d9fac0ad06babd3ab79a9ec5bd66352fe"
+checksum = "d5d4880e6d634d3d029d65fa016038e788cc728a17b782684726fb34ee140caf"
 dependencies = [
  "libdeflate-sys",
 ]
 
+[[package]]
+name = "libloading"
+version = "0.8.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d7c4b02199fee7c5d21a5ae7d8cfa79a6ef5bb2fc834d6e9058e89c825efdc55"
+dependencies = [
+ "cfg-if",
+ "windows-link",
+]
+
 [[package]]
 name = "libm"
-version = "0.2.8"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f9fbbcab51052fe104eb5e5d351cf728d30a5be1fe14d9be8a3b097481fb97de"
+
+[[package]]
+name = "libz-ng-sys"
+version = "1.1.23"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
+checksum = "7bf914b7dd154ca9193afec311d8e39345c1bd93b48b3faa77329f0db8f553c0"
+dependencies = [
+ "cmake",
+ "libc",
+]
 
 [[package]]
 name = "libz-sys"
-version = "1.1.12"
+version = "1.1.23"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d97137b25e321a73eef1418d1d5d2eda4d77e12813f8e6dead84bc52c5870a7b"
+checksum = "15d118bbf3771060e7311cc7bb0545b01d08a8b4a7de949198dec1fa0ca1c0f7"
 dependencies = [
  "cc",
  "cmake",
@@ -792,25 +1089,30 @@ checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
 
 [[package]]
 name = "linux-raw-sys"
-version = "0.4.10"
+version = "0.11.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "df1d3c3b53da64cf5760482273a98e575c651a67eec7f77df96b5b642de8f039"
+
+[[package]]
+name = "litemap"
+version = "0.8.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da2479e8c062e40bf0066ffa0bc823de0a9368974af99c9f6df941d2c231e03f"
+checksum = "6373607a59f0be73a39b6fe456b8192fcc3585f602af20751600e974dd455e77"
 
 [[package]]
 name = "lock_api"
-version = "0.4.10"
+version = "0.4.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16"
+checksum = "224399e74b87b5f3557511d98dff8b14089b3dadafcab6bb93eab67d3aace965"
 dependencies = [
- "autocfg",
  "scopeguard",
 ]
 
 [[package]]
 name = "log"
-version = "0.4.20"
+version = "0.4.29"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f"
+checksum = "5e5032e24019045c762d3c0f28f5b6b8bbf38563a65908389bf7978758920897"
 
 [[package]]
 name = "lru_time_cache"
@@ -818,22 +1120,11 @@ version = "0.11.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9106e1d747ffd48e6be5bb2d97fa706ed25b144fbee4d5c02eae110cd8d6badd"
 
-[[package]]
-name = "lzma-sys"
-version = "0.1.20"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27"
-dependencies = [
- "cc",
- "libc",
- "pkg-config",
-]
-
 [[package]]
 name = "matrixmultiply"
-version = "0.3.8"
+version = "0.3.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7574c1cf36da4798ab73da5b215bbf444f50718207754cb522201d78d1cd0ff2"
+checksum = "a06de3016e9fae57a36fd14dba131fccf49f74b40b7fbdb472f96e361ec71a08"
 dependencies = [
  "autocfg",
  "rawpointer",
@@ -841,26 +1132,24 @@ dependencies = [
 
 [[package]]
 name = "memchr"
-version = "2.6.4"
+version = "2.7.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f665ee40bc4a3c5590afb1e9677db74a508659dfd71e126420da8274909a0167"
+checksum = "f52b00d39961fc5b2736ea853c9cc86238e165017a493d1d5c8eac6bdc4cc273"
 
 [[package]]
-name = "memoffset"
-version = "0.9.0"
+name = "minimal-lexical"
+version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c"
-dependencies = [
- "autocfg",
-]
+checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.1"
+version = "0.8.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7"
+checksum = "1fa76a2c86f704bdb222d66965fb3d63269ce38518b83cb0575fca855ebb6316"
 dependencies = [
- "adler",
+ "adler2",
+ "simd-adler32",
 ]
 
 [[package]]
@@ -884,7 +1173,7 @@ dependencies = [
  "num-complex",
  "num-rational",
  "num-traits",
- "rand",
+ "rand 0.8.5",
  "rand_distr",
  "simba",
  "typenum",
@@ -896,8 +1185,8 @@ version = "0.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "01fcc0b8149b4632adc89ac3b7b31a12fb6099a0317a4eb2ebff574ef7de7218"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "syn 1.0.109",
 ]
 
@@ -907,7 +1196,7 @@ version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6a51313c5820b0b02bd422f4b44776fbf47961755c74ce64afc73bfad10226c3"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.16",
 ]
 
 [[package]]
@@ -932,41 +1221,49 @@ dependencies = [
  "rustc_version 0.1.7",
 ]
 
+[[package]]
+name = "nom"
+version = "7.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a"
+dependencies = [
+ "memchr",
+ "minimal-lexical",
+]
+
 [[package]]
 name = "num-complex"
-version = "0.4.4"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1ba157ca0885411de85d6ca030ba7e2a83a28636056c7c699b07c8b6f7383214"
+checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495"
 dependencies = [
  "num-traits",
 ]
 
 [[package]]
 name = "num-integer"
-version = "0.1.45"
+version = "0.1.46"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9"
+checksum = "7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f"
 dependencies = [
- "autocfg",
  "num-traits",
 ]
 
 [[package]]
 name = "num-rational"
-version = "0.4.1"
+version = "0.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0638a1c9d0a3c0914158145bc76cff373a75a627e6ecbfb71cbe6f453a5a19b0"
+checksum = "f83d14da390562dca69fc84082e73e548e1ad308d24accdedd2720017cb37824"
 dependencies = [
- "autocfg",
  "num-integer",
  "num-traits",
 ]
 
 [[package]]
 name = "num-traits"
-version = "0.2.17"
+version = "0.2.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c"
+checksum = "071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841"
 dependencies = [
  "autocfg",
  "libm",
@@ -974,56 +1271,40 @@ dependencies = [
 
 [[package]]
 name = "num_cpus"
-version = "1.16.0"
+version = "1.17.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43"
+checksum = "91df4bbde75afed763b708b7eee1e8e7651e02d97f6d5dd763e89367e957b23b"
 dependencies = [
- "hermit-abi 0.3.3",
+ "hermit-abi 0.5.2",
  "libc",
 ]
 
 [[package]]
 name = "once_cell"
-version = "1.18.0"
+version = "1.21.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d"
+checksum = "42f5e15c9953c5e4ccceeb2e7382a716482c34515315f7b03532b8b4e8393d2d"
 
 [[package]]
-name = "openssl-src"
-version = "300.1.5+3.1.3"
+name = "once_cell_polyfill"
+version = "1.70.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "559068e4c12950d7dcaa1857a61725c0d38d4fc03ff8e070ab31a75d6e316491"
-dependencies = [
- "cc",
-]
-
-[[package]]
-name = "openssl-sys"
-version = "0.9.93"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "db4d56a4c0478783083cfafcc42493dd4a981d41669da64b4572a2a089b51b1d"
-dependencies = [
- "cc",
- "libc",
- "openssl-src",
- "pkg-config",
- "vcpkg",
-]
+checksum = "384b8ab6d37215f3c5301a95a4accb5d64aa607f1fcb26a11b5303878451b4fe"
 
 [[package]]
 name = "ordered-float"
-version = "1.1.1"
+version = "5.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3305af35278dd29f46fcdd139e0b1fbfae2153f0e5928b39b035542dd31e37b7"
+checksum = "7f4779c6901a562440c3786d08192c6fbda7c1c2060edd10006b05ee35d10f2d"
 dependencies = [
  "num-traits",
 ]
 
 [[package]]
 name = "paste"
-version = "1.0.14"
+version = "1.0.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c"
+checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a"
 
 [[package]]
 name = "perbase"
@@ -1037,7 +1318,7 @@ dependencies = [
  "env_logger",
  "grep-cli",
  "gzp",
- "itertools",
+ "itertools 0.14.0",
  "lazy_static",
  "log",
  "lru_time_cache",
@@ -1050,58 +1331,86 @@ dependencies = [
  "serde",
  "smartstring",
  "structopt",
- "strum 0.27.1",
+ "strum 0.27.2",
  "tempfile",
  "termcolor",
 ]
 
 [[package]]
 name = "percent-encoding"
-version = "2.3.0"
+version = "2.3.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9b2a4787296e9989611394c33f193f676704af1686e70b8f8033ab5ba9a35a94"
+checksum = "9b4f627cb1b25917193a259e49bdad08f671f8d9708acfd5fe0a8c1455d87220"
 
 [[package]]
 name = "petgraph"
-version = "0.6.4"
+version = "0.6.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e1d3afd2628e69da2be385eb6f2fd57c8ac7977ceeff6dc166ff1657b0e386a9"
+checksum = "b4c5cc86750666a3ed20bdaf5ca2a0344f9c67674cae0515bec2da16fbaa47db"
 dependencies = [
  "fixedbitset",
  "indexmap",
 ]
 
 [[package]]
-name = "pin-project"
-version = "1.1.3"
+name = "pin-project-lite"
+version = "0.2.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fda4ed1c6c173e3fc7a83629421152e01d7b1f9b7f65fb301e490e8cfc656422"
+checksum = "3b3cff922bd51709b605d9ead9aa71031d81447142d828eb4a6eba76fe619f9b"
+
+[[package]]
+name = "pin-utils"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184"
+
+[[package]]
+name = "pkg-config"
+version = "0.3.32"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7edddbd0b52d732b21ad9a5fab5c704c14cd949e5e9a1ec5929a24fded1b904c"
+
+[[package]]
+name = "portable-atomic"
+version = "1.11.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f84267b20a16ea918e43c6a88433c2d54fa145c92a811b5b047ccbe153674483"
+
+[[package]]
+name = "portable-atomic-util"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d8a2f0d8d040d7848a709caf78912debcc3f33ee4b3cac47d73d1e1069e83507"
 dependencies = [
- "pin-project-internal",
+ "portable-atomic",
 ]
 
 [[package]]
-name = "pin-project-internal"
-version = "1.1.3"
+name = "potential_utf"
+version = "0.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4359fd9c9171ec6e8c62926d6faaf553a8dc3f64e1507e76da7911b4f6a04405"
+checksum = "b73949432f5e2a09657003c25bca5e19a0e9c84f8058ca374f49e0ebe605af77"
 dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.38",
+ "zerovec",
 ]
 
 [[package]]
-name = "pkg-config"
-version = "0.3.27"
+name = "ppv-lite86"
+version = "0.2.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964"
+checksum = "85eae3c4ed2f50dcfe72643da4befc30deadb458a9b590d720cde2f2b1e97da9"
+dependencies = [
+ "zerocopy",
+]
 
 [[package]]
-name = "ppv-lite86"
-version = "0.2.17"
+name = "proc-macro-crate"
+version = "3.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
+checksum = "219cb19e96be00ab2e37d6e299658a0cfa83e52429179969b0f0121b4ac46983"
+dependencies = [
+ "toml_edit",
+]
 
 [[package]]
 name = "proc-macro-error"
@@ -1110,8 +1419,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c"
 dependencies = [
  "proc-macro-error-attr",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "syn 1.0.109",
  "version_check",
 ]
@@ -1122,35 +1431,65 @@ version = "1.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "version_check",
 ]
 
+[[package]]
+name = "proc-macro-error-attr2"
+version = "2.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "96de42df36bb9bba5542fe9f1a054b8cc87e172759a1868aa05c1f3acc89dfc5"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+]
+
+[[package]]
+name = "proc-macro-error2"
+version = "2.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "11ec05c52be0a07b08061f7dd003e7d7092e0472bc731b4af7bb1ef876109802"
+dependencies = [
+ "proc-macro-error-attr2",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
+
 [[package]]
 name = "proc-macro2"
-version = "1.0.69"
+version = "0.4.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cf3d2011ab5c909338f7887f4fc896d35932e29146c12c8d01da6b22a80ba759"
+dependencies = [
+ "unicode-xid",
+]
+
+[[package]]
+name = "proc-macro2"
+version = "1.0.103"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "134c189feb4956b20f6f547d2cf727d4c0fe06722b20a0eec87ed445a97f92da"
+checksum = "5ee95bc4ef87b8d5ba32e8b7714ccc834865276eab0aed5c9958d00ec45f49e8"
 dependencies = [
  "unicode-ident",
 ]
 
 [[package]]
 name = "proptest"
-version = "1.3.1"
+version = "1.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7c003ac8c77cb07bb74f5f198bce836a689bcd5a42574612bf14d17bfd08c20e"
+checksum = "bee689443a2bd0a16ab0348b52ee43e3b2d1b1f931c8aa5c9f8de4c86fbe8c40"
 dependencies = [
  "bit-set",
  "bit-vec",
- "bitflags 2.4.0",
- "lazy_static",
+ "bitflags 2.10.0",
  "num-traits",
- "rand",
- "rand_chacha",
+ "rand 0.9.2",
+ "rand_chacha 0.9.0",
  "rand_xorshift",
- "regex-syntax 0.7.5",
+ "regex-syntax",
  "rusty-fork",
  "tempfile",
  "unarray",
@@ -1164,13 +1503,28 @@ checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
 
 [[package]]
 name = "quote"
-version = "1.0.33"
+version = "0.6.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6ce23b6b870e8f94f81fb0a363d65d86675884b34a09043c81e5562f11c1f8e1"
+dependencies = [
+ "proc-macro2 0.4.30",
+]
+
+[[package]]
+name = "quote"
+version = "1.0.42"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5267fca4496028628a95160fc423a33e8b2e6af8a5302579e322e4b520293cae"
+checksum = "a338cc41d27e6cc6dce6cefc13a0729dfbb81c262b1f519331575dd80ef3067f"
 dependencies = [
- "proc-macro2",
+ "proc-macro2 1.0.103",
 ]
 
+[[package]]
+name = "r-efi"
+version = "5.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "69cdb34c158ceb288df11e18b4bd39de994f6657d83847bdffdbd7f346754b0f"
+
 [[package]]
 name = "rand"
 version = "0.8.5"
@@ -1178,8 +1532,18 @@ 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 = "0.9.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6db2770f06117d490610c7488547d543617b21bfa07796d7a12f6f1bd53850d1"
+dependencies = [
+ "rand_chacha 0.9.0",
+ "rand_core 0.9.3",
 ]
 
 [[package]]
@@ -1189,7 +1553,17 @@ 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 0.9.3",
 ]
 
 [[package]]
@@ -1198,7 +1572,16 @@ version = "0.6.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.16",
+]
+
+[[package]]
+name = "rand_core"
+version = "0.9.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "99d9a13982dcf210057a8a78572b2217b667c3beacbf3a0d8b454f6f82837d38"
+dependencies = [
+ "getrandom 0.3.4",
 ]
 
 [[package]]
@@ -1208,16 +1591,16 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32cb0b9bc82b0a0876c2dd994a7e7a2683d3e7390ca40e6886785ef0c7e3ee31"
 dependencies = [
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
 name = "rand_xorshift"
-version = "0.3.0"
+version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d25bf25ec5ae4a3f1b92f929810509a2f53d7dca2f50b794ff57e3face536c8f"
+checksum = "513962919efc330f829edb2535844d1b912b0fbe2ca165d613e4e8788bb05a5a"
 dependencies = [
- "rand_core",
+ "rand_core 0.9.3",
 ]
 
 [[package]]
@@ -1228,9 +1611,9 @@ checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
 
 [[package]]
 name = "rayon"
-version = "1.8.0"
+version = "1.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c27db03db7734835b3f53954b534c91069375ce6ccaa2e065441e07d9b6cdb1"
+checksum = "368f01d005bf8fd9b1206fb6fa653e6c4a81ceb1466406b81792d87c5677a58f"
 dependencies = [
  "either",
  "rayon-core",
@@ -1238,101 +1621,115 @@ dependencies = [
 
 [[package]]
 name = "rayon-core"
-version = "1.12.0"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ce3fb6ad83f861aac485e76e1985cd109d9a3713802152be56c3b1f0e0658ed"
+checksum = "22e18b0f0062d30d4230b2e85ff77fdfe4326feb054b9783a3460d8435c8ab91"
 dependencies = [
  "crossbeam-deque",
  "crossbeam-utils",
 ]
 
-[[package]]
-name = "redox_syscall"
-version = "0.3.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29"
-dependencies = [
- "bitflags 1.3.2",
-]
-
 [[package]]
 name = "regex"
-version = "1.10.0"
+version = "1.12.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d119d7c7ca818f8a53c300863d4f87566aac09943aef5b355bb83969dae75d87"
+checksum = "843bc0191f75f3e22651ae5f1e72939ab2f72a4bc30fa80a066bd66edefc24d4"
 dependencies = [
  "aho-corasick",
  "memchr",
  "regex-automata",
- "regex-syntax 0.8.0",
+ "regex-syntax",
 ]
 
 [[package]]
 name = "regex-automata"
-version = "0.4.1"
+version = "0.4.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "465c6fc0621e4abc4187a2bda0937bfd4f722c2730b29562e19689ea796c9a4b"
+checksum = "5276caf25ac86c8d810222b3dbb938e512c55c6831a10f3e6ed1c93b84041f1c"
 dependencies = [
  "aho-corasick",
  "memchr",
- "regex-syntax 0.8.0",
+ "regex-syntax",
 ]
 
 [[package]]
 name = "regex-syntax"
-version = "0.7.5"
+version = "0.8.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da"
+checksum = "7a2d987857b319362043e95f5353c0535c1f58eec5336fdfcf626430af7def58"
 
 [[package]]
-name = "regex-syntax"
-version = "0.8.0"
+name = "relative-path"
+version = "1.9.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c3cbb081b9784b07cceb8824c8583f86db4814d172ab043f3c23f7dc600bf83d"
+checksum = "ba39f3699c378cd8970968dcbff9c43159ea4cfbd88d43c00b22f2ef10a435d2"
 
 [[package]]
 name = "rstest"
-version = "0.11.0"
+version = "0.26.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f5a3193c063baaa2a95a33f03035c8a72b83d97a54916055ba22d35ed3839d49"
+dependencies = [
+ "futures-timer",
+ "futures-util",
+ "rstest_macros",
+]
+
+[[package]]
+name = "rstest_macros"
+version = "0.26.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2288c66aeafe3b2ed227c981f364f9968fa952ef0b30e84ada4486e7ee24d00a"
+checksum = "9c845311f0ff7951c5506121a9ad75aec44d083c31583b2ea5a30bcb0b0abba0"
 dependencies = [
  "cfg-if",
- "proc-macro2",
- "quote",
- "rustc_version 0.4.0",
- "syn 1.0.109",
+ "glob",
+ "proc-macro-crate",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "regex",
+ "relative-path",
+ "rustc_version 0.4.1",
+ "syn 2.0.111",
+ "unicode-ident",
 ]
 
 [[package]]
 name = "rust-htslib"
-version = "0.39.5"
+version = "0.51.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "239ef7334dbf59acd56b7a6fa62a525ed7e36d6239a686ed4ff61bc794108e53"
+checksum = "354416dd2300ff9e7aff8ddc747c875d6c5086f83c2cb2599f3692421c2b77fd"
 dependencies = [
  "bio-types",
  "byteorder",
  "custom_derive",
- "derive-new",
+ "derive-new 0.7.0",
  "hts-sys",
  "ieee754",
  "lazy_static",
  "libc",
+ "libz-sys",
  "linear-map",
  "newtype_derive",
  "regex",
- "thiserror",
+ "thiserror 2.0.17",
  "url",
 ]
 
 [[package]]
 name = "rust-lapper"
-version = "1.1.0"
+version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ee43d8e721ac803031dbab6a944b957b49a3b11eadbc099880c8aaaebf23ed27"
+checksum = "2274b9cc4f205bc0945b7be3e4fc1a102b0b7119ba6482faaedb9c4f76dde5d1"
 dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "rustc-hash"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2"
+
 [[package]]
 name = "rustc_version"
 version = "0.1.7"
@@ -1344,20 +1741,20 @@ dependencies = [
 
 [[package]]
 name = "rustc_version"
-version = "0.4.0"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366"
+checksum = "cfcb3a22ef46e85b45de6ee7e79d063319ebb6594faafcf1c225ea92ab6e9b92"
 dependencies = [
- "semver 1.0.20",
+ "semver 1.0.27",
 ]
 
 [[package]]
 name = "rustix"
-version = "0.38.18"
+version = "1.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a74ee2d7c2581cd139b42447d7d9389b889bdaad3a73f1ebb16f2a3237bb19c"
+checksum = "cd15f8a2c5551a84d56efdc1cd049089e409ac19a3072d5037a17fd70719ff3e"
 dependencies = [
- "bitflags 2.4.0",
+ "bitflags 2.10.0",
  "errno",
  "libc",
  "linux-raw-sys",
@@ -1366,15 +1763,15 @@ dependencies = [
 
 [[package]]
 name = "rustversion"
-version = "1.0.14"
+version = "1.0.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4"
+checksum = "b39cdef0fa800fc44525c84ccb54a029961a8215f9619753635a9c0d2538d46d"
 
 [[package]]
 name = "rusty-fork"
-version = "0.3.0"
+version = "0.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cb3dcc6e454c328bb824492db107ab7c0ae8fcffe4ad210136ef014458c1bc4f"
+checksum = "cc6bf79ff24e648f6da1f8d1f011e9cac26491b619e6b9280f2b47f1774e6ee2"
 dependencies = [
  "fnv",
  "quick-error",
@@ -1384,18 +1781,9 @@ dependencies = [
 
 [[package]]
 name = "ryu"
-version = "1.0.15"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1ad4cc8da4ef723ed60bced201181d83791ad433213d8c24efffda1eec85d741"
-
-[[package]]
-name = "same-file"
-version = "1.0.6"
+version = "1.0.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502"
-dependencies = [
- "winapi-util",
-]
+checksum = "28d3b2b1366ec20994f1fd18c3c594f05c5dd4bc44d8bb0c1c632c8d6829481f"
 
 [[package]]
 name = "scopeguard"
@@ -1411,30 +1799,46 @@ checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
 [[package]]
 name = "semver"
-version = "1.0.20"
+version = "1.0.27"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "836fa6a3e1e547f9a2c4040802ec865b5d85f4014efe00555d7090a3dcaa1090"
+checksum = "d767eb0aabc880b29956c35734170f26ed551a859dbd361d140cdbeca61ab1e2"
 
 [[package]]
 name = "serde"
-version = "1.0.188"
+version = "1.0.228"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9a8e94ea7f378bd32cbbd37198a4a91436180c5bb472411e48b5ec2e2124ae9e"
+dependencies = [
+ "serde_core",
+ "serde_derive",
+]
+
+[[package]]
+name = "serde_core"
+version = "1.0.228"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cf9e0fcba69a370eed61bcf2b728575f726b50b55cba78064753d708ddc7549e"
+checksum = "41d385c7d4ca58e59fc732af25c3983b67ac852c1a25000afe1175de458b67ad"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.188"
+version = "1.0.228"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4eca7ac642d82aa35b60049a6eccb4be6be75e599bd2e9adb5f875a737654af2"
+checksum = "d540f220d3187173da220f885ab66608367b6574e925011a9353e4badda91d79"
 dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.38",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
 ]
 
+[[package]]
+name = "shlex"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
+
 [[package]]
 name = "simba"
 version = "0.5.1"
@@ -1447,6 +1851,24 @@ dependencies = [
  "paste",
 ]
 
+[[package]]
+name = "simd-adler32"
+version = "0.3.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e320a6c5ad31d271ad523dcf3ad13e2767ad8b1cb8f047f75a8aeaf8da139da2"
+
+[[package]]
+name = "slab"
+version = "0.4.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7a2ae44ef20feb57a68b23d846850f861394c2e02dc425a50098ae8c90267589"
+
+[[package]]
+name = "smallvec"
+version = "1.15.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "67b1b7a3b5fe4f1376887184045fcf45c69e92af734b7aaddc05fb777b6fbd03"
+
 [[package]]
 name = "smartstring"
 version = "1.0.1"
@@ -1468,6 +1890,12 @@ dependencies = [
  "lock_api",
 ]
 
+[[package]]
+name = "stable_deref_trait"
+version = "1.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6ce2be8dc25455e1f91df71bfa12ad37d7af1092ae736f3a6cd0e37bc7810596"
+
 [[package]]
 name = "static_assertions"
 version = "1.1.0"
@@ -1484,7 +1912,7 @@ dependencies = [
  "lazy_static",
  "nalgebra",
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -1512,8 +1940,8 @@ checksum = "dcb5ae327f9cc13b68763b5749770cb9e048a99bd9dfdfa58d0cf05d5f64afe0"
 dependencies = [
  "heck 0.3.3",
  "proc-macro-error",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "syn 1.0.109",
 ]
 
@@ -1525,50 +1953,47 @@ checksum = "cae14b91c7d11c9a851d3fbc80a963198998c2a64eec840477fa92d8ce9b70bb"
 
 [[package]]
 name = "strum"
-version = "0.27.1"
+version = "0.27.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f64def088c51c9510a8579e3c5d67c65349dcf755e5479ad3d010aa6454e2c32"
+checksum = "af23d6f6c1a224baef9d3f61e287d2761385a5b88fdab4eb4c6f11aeb54c4bcf"
 dependencies = [
- "strum_macros 0.27.1",
+ "strum_macros 0.27.2",
 ]
 
 [[package]]
 name = "strum_macros"
-version = "0.23.1"
+version = "0.26.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5bb0dc7ee9c15cea6199cde9a127fa16a4c5819af85395457ad72d68edc85a38"
+checksum = "4c6bee85a5a24955dc440386795aa378cd9cf82acd5f764469152d2270e581be"
 dependencies = [
- "heck 0.3.3",
- "proc-macro2",
- "quote",
+ "heck 0.5.0",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "rustversion",
- "syn 1.0.109",
+ "syn 2.0.111",
 ]
 
 [[package]]
 name = "strum_macros"
-version = "0.25.2"
+version = "0.27.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ad8d03b598d3d0fff69bf533ee3ef19b8eeb342729596df84bcc7e1f96ec4059"
+checksum = "7695ce3845ea4b33927c055a39dc438a45b059f7c1b3d91d38d10355fb8cbca7"
 dependencies = [
- "heck 0.4.1",
- "proc-macro2",
- "quote",
- "rustversion",
- "syn 2.0.38",
+ "heck 0.5.0",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
 ]
 
 [[package]]
-name = "strum_macros"
-version = "0.27.1"
+name = "syn"
+version = "0.15.44"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c77a8c5abcaf0f9ce05d62342b7d298c346515365c36b673df4ebe3ced01fde8"
+checksum = "9ca4b3b69a77cbe1ffc9e198781b7acb0c7365a883670e8f1c1bc66fba79a5c5"
 dependencies = [
- "heck 0.5.0",
- "proc-macro2",
- "quote",
- "rustversion",
- "syn 2.0.38",
+ "proc-macro2 0.4.30",
+ "quote 0.6.13",
+ "unicode-xid",
 ]
 
 [[package]]
@@ -1577,40 +2002,51 @@ version = "1.0.109"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "unicode-ident",
 ]
 
 [[package]]
 name = "syn"
-version = "2.0.38"
+version = "2.0.111"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e96b79aaa137db8f61e26363a0c9b47d8b4ec75da28b7d1d614c2303e232408b"
+checksum = "390cc9a294ab71bdb1aa2e99d13be9c753cd2d7bd6560c77118597410c4d2e87"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
  "unicode-ident",
 ]
 
+[[package]]
+name = "synstructure"
+version = "0.13.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "728a70f3dbaf5bab7f0c4b1ac8d7ae5ea60a4b5549c8a5914361c99147a709d2"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
+
 [[package]]
 name = "tempfile"
-version = "3.8.0"
+version = "3.23.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cb94d2f3cc536af71caac6b6fcebf65860b347e7ce0cc9ebe8f70d3e521054ef"
+checksum = "2d31c77bdf42a745371d260a26ca7163f1e0924b64afa0b688e61b5a9fa02f16"
 dependencies = [
- "cfg-if",
  "fastrand",
- "redox_syscall",
+ "getrandom 0.3.4",
+ "once_cell",
  "rustix",
  "windows-sys",
 ]
 
 [[package]]
 name = "termcolor"
-version = "1.3.0"
+version = "1.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6093bad37da69aab9d123a8091e4be0aa4a03e4d601ec641c327398315f62b64"
+checksum = "06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755"
 dependencies = [
  "winapi-util",
 ]
@@ -1626,38 +2062,83 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.49"
+version = "1.0.69"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52"
+dependencies = [
+ "thiserror-impl 1.0.69",
+]
+
+[[package]]
+name = "thiserror"
+version = "2.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1177e8c6d7ede7afde3585fd2513e611227efd6481bd78d2e82ba1ce16557ed4"
+checksum = "f63587ca0f12b72a0600bcba1d40081f830876000bb46dd2337a3051618f4fc8"
 dependencies = [
- "thiserror-impl",
+ "thiserror-impl 2.0.17",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.49"
+version = "1.0.69"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "10712f02019e9288794769fba95cd6847df9874d49d871d062172f9dd41bc4cc"
+checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1"
 dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.38",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
 ]
 
 [[package]]
-name = "tinyvec"
-version = "1.6.0"
+name = "thiserror-impl"
+version = "2.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50"
+checksum = "3ff15c8ecd7de3849db632e14d18d2571fa09dfc5ed93479bc4485c7a517c913"
 dependencies = [
- "tinyvec_macros",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
 ]
 
 [[package]]
-name = "tinyvec_macros"
-version = "0.1.1"
+name = "tinystr"
+version = "0.8.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "42d3e9c45c09de15d06dd8acf5f4e0e399e85927b7f00711024eb7ae10fa4869"
+dependencies = [
+ "displaydoc",
+ "zerovec",
+]
+
+[[package]]
+name = "toml_datetime"
+version = "0.7.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f2cdb639ebbc97961c51720f858597f7f24c4fc295327923af55b74c3c724533"
+dependencies = [
+ "serde_core",
+]
+
+[[package]]
+name = "toml_edit"
+version = "0.23.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5d7cbc3b4b49633d57a0509303158ca50de80ae32c265093b24c414705807832"
+dependencies = [
+ "indexmap",
+ "toml_datetime",
+ "toml_parser",
+ "winnow",
+]
+
+[[package]]
+name = "toml_parser"
+version = "1.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
+checksum = "c0cbe268d35bdb4bb5a56a2de88d0ad0eb70af5384a99d648cd4b3d04039800e"
+dependencies = [
+ "winnow",
+]
 
 [[package]]
 name = "triple_accel"
@@ -1667,9 +2148,9 @@ checksum = "22048bc95dfb2ffd05b1ff9a756290a009224b60b2f0e7525faeee7603851e63"
 
 [[package]]
 name = "typenum"
-version = "1.17.0"
+version = "1.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
+checksum = "562d481066bde0658276a35467c4af00bdc6ee726305698a55b86e61d7ad82bb"
 
 [[package]]
 name = "unarray"
@@ -1677,50 +2158,54 @@ version = "0.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "eaea85b334db583fe3274d12b4cd1880032beab409c0d774be044d4480ab9a94"
 
-[[package]]
-name = "unicode-bidi"
-version = "0.3.13"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460"
-
 [[package]]
 name = "unicode-ident"
-version = "1.0.12"
+version = "1.0.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
+checksum = "9312f7c4f6ff9069b165498234ce8be658059c6728633667c526e27dc2cf1df5"
 
 [[package]]
-name = "unicode-normalization"
-version = "0.1.22"
+name = "unicode-segmentation"
+version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921"
-dependencies = [
- "tinyvec",
-]
+checksum = "f6ccf251212114b54433ec949fd6a7841275f9ada20dddd2f29e9ceea4501493"
 
 [[package]]
-name = "unicode-segmentation"
-version = "1.10.1"
+name = "unicode-width"
+version = "0.1.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1dd624098567895118886609431a7c3b8f516e41d30e0643f03d94592a147e36"
+checksum = "7dd6e30e90baa6f72411720665d41d89b9a3d039dc45b8faea1ddd07f617f6af"
 
 [[package]]
-name = "unicode-width"
-version = "0.1.11"
+name = "unicode-xid"
+version = "0.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e51733f11c9c4f72aa0c160008246859e340b00807569a0da0e7a1079b27ba85"
+checksum = "fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc"
 
 [[package]]
 name = "url"
-version = "2.4.1"
+version = "2.5.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "143b538f18257fac9cad154828a57c6bf5157e1aa604d4816b5995bf6de87ae5"
+checksum = "08bc136a29a3d1758e07a9cca267be308aeebf5cfd5a10f3f67ab2097683ef5b"
 dependencies = [
  "form_urlencoded",
  "idna",
  "percent-encoding",
+ "serde",
 ]
 
+[[package]]
+name = "utf8_iter"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6c140620e7ffbb22c2dee59cafe6084a59b5ffc27a8859a5f0d494b5d52b6be"
+
+[[package]]
+name = "utf8parse"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
+
 [[package]]
 name = "vcpkg"
 version = "0.2.15"
@@ -1738,84 +2223,78 @@ dependencies = [
 
 [[package]]
 name = "version_check"
-version = "0.9.4"
+version = "0.9.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
+checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a"
 
 [[package]]
 name = "wait-timeout"
-version = "0.2.0"
+version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9f200f5b12eb75f8c1ed65abd4b2db8a6e1b138a20de009dacee265a2498f3f6"
+checksum = "09ac3b126d3914f9849036f826e054cbabdc8519970b8998ddaf3b5bd3c65f11"
 dependencies = [
  "libc",
 ]
 
 [[package]]
 name = "wasi"
-version = "0.11.0+wasi-snapshot-preview1"
+version = "0.11.1+wasi-snapshot-preview1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
+checksum = "ccf3ec651a847eb01de73ccad15eb7d99f80485de043efb2f370cd654f4ea44b"
 
 [[package]]
-name = "wasm-bindgen"
-version = "0.2.87"
+name = "wasip2"
+version = "1.0.1+wasi-0.2.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7706a72ab36d8cb1f80ffbf0e071533974a60d0a308d01a5d0375bf60499a342"
+checksum = "0562428422c63773dad2c345a1882263bbf4d65cf3f42e90921f787ef5ad58e7"
 dependencies = [
- "cfg-if",
- "wasm-bindgen-macro",
+ "wit-bindgen",
 ]
 
 [[package]]
-name = "wasm-bindgen-backend"
-version = "0.2.87"
+name = "wasm-bindgen"
+version = "0.2.106"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ef2b6d3c510e9625e5fe6f509ab07d66a760f0885d858736483c32ed7809abd"
+checksum = "0d759f433fa64a2d763d1340820e46e111a7a5ab75f993d1852d70b03dbb80fd"
 dependencies = [
- "bumpalo",
- "log",
+ "cfg-if",
  "once_cell",
- "proc-macro2",
- "quote",
- "syn 2.0.38",
+ "rustversion",
+ "wasm-bindgen-macro",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.87"
+version = "0.2.106"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dee495e55982a3bd48105a7b947fd2a9b4a8ae3010041b9e0faab3f9cd028f1d"
+checksum = "48cb0d2638f8baedbc542ed444afc0644a29166f1595371af4fecf8ce1e7eeb3"
 dependencies = [
- "quote",
+ "quote 1.0.42",
  "wasm-bindgen-macro-support",
 ]
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.87"
+version = "0.2.106"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b"
+checksum = "cefb59d5cd5f92d9dcf80e4683949f15ca4b511f4ac0a6e14d4e1ac60c6ecd40"
 dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.38",
- "wasm-bindgen-backend",
+ "bumpalo",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.87"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ca6ad05a4870b2bf5fe995117d3728437bd27d7cd5f06f13c17443ef369775a1"
-
-[[package]]
-name = "winapi"
-version = "0.2.8"
+version = "0.2.106"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "167dc9d6949a9b857f3451275e911c3f44255842c1f7a76f33c55103a909087a"
+checksum = "cbc538057e648b67f72a982e708d485b2efa771e1ac05fec311f9f63e5800db4"
+dependencies = [
+ "unicode-ident",
+]
 
 [[package]]
 name = "winapi"
@@ -1827,12 +2306,6 @@ dependencies = [
  "winapi-x86_64-pc-windows-gnu",
 ]
 
-[[package]]
-name = "winapi-build"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2d315eee3b34aca4797b2da6b13ed88266e6d612562a0c46390af8299fc699bc"
-
 [[package]]
 name = "winapi-i686-pc-windows-gnu"
 version = "0.4.0"
@@ -1841,11 +2314,11 @@ checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
 
 [[package]]
 name = "winapi-util"
-version = "0.1.6"
+version = "0.1.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596"
+checksum = "c2a7b1c03c876122aa43f3020e6c3c3ee5c05081c9a00739faf7503aeba10d22"
 dependencies = [
- "winapi 0.3.9",
+ "windows-sys",
 ]
 
 [[package]]
@@ -1854,68 +2327,135 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
 
+[[package]]
+name = "windows-link"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f0805222e57f7521d6a62e36fa9163bc891acd422f971defe97d64e70d0a4fe5"
+
 [[package]]
 name = "windows-sys"
-version = "0.48.0"
+version = "0.61.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ae137229bcbd6cdf0f7b80a31df61766145077ddf49416a728b02cb3921ff3fc"
+dependencies = [
+ "windows-link",
+]
+
+[[package]]
+name = "winnow"
+version = "0.7.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5a5364e9d77fcdeeaa6062ced926ee3381faa2ee02d3eb83a5c27a8825540829"
+dependencies = [
+ "memchr",
+]
+
+[[package]]
+name = "wit-bindgen"
+version = "0.46.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f17a85883d4e6d00e8a97c586de764dabcc06133f7f1d55dce5cdc070ad7fe59"
+
+[[package]]
+name = "writeable"
+version = "0.6.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9edde0db4769d2dc68579893f2306b26c6ecfbe0ef499b013d731b7b9247e0b9"
+
+[[package]]
+name = "yoke"
+version = "0.8.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9"
+checksum = "72d6e5c6afb84d73944e5cedb052c4680d5657337201555f9f2a16b7406d4954"
 dependencies = [
- "windows-targets",
+ "stable_deref_trait",
+ "yoke-derive",
+ "zerofrom",
 ]
 
 [[package]]
-name = "windows-targets"
-version = "0.48.5"
+name = "yoke-derive"
+version = "0.8.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
+checksum = "b659052874eb698efe5b9e8cf382204678a0086ebf46982b79d6ca3182927e5d"
 dependencies = [
- "windows_aarch64_gnullvm",
- "windows_aarch64_msvc",
- "windows_i686_gnu",
- "windows_i686_msvc",
- "windows_x86_64_gnu",
- "windows_x86_64_gnullvm",
- "windows_x86_64_msvc",
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+ "synstructure",
 ]
 
 [[package]]
-name = "windows_aarch64_gnullvm"
-version = "0.48.5"
+name = "zerocopy"
+version = "0.8.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
+checksum = "fd74ec98b9250adb3ca554bdde269adf631549f51d8a8f8f0a10b50f1cb298c3"
+dependencies = [
+ "zerocopy-derive",
+]
 
 [[package]]
-name = "windows_aarch64_msvc"
-version = "0.48.5"
+name = "zerocopy-derive"
+version = "0.8.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
+checksum = "d8a8d209fdf45cf5138cbb5a506f6b52522a25afccc534d1475dad8e31105c6a"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
 
 [[package]]
-name = "windows_i686_gnu"
-version = "0.48.5"
+name = "zerofrom"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
+checksum = "50cc42e0333e05660c3587f3bf9d0478688e15d870fab3346451ce7f8c9fbea5"
+dependencies = [
+ "zerofrom-derive",
+]
 
 [[package]]
-name = "windows_i686_msvc"
-version = "0.48.5"
+name = "zerofrom-derive"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
+checksum = "d71e5d6e06ab090c67b5e44993ec16b72dcbaabc526db883a360057678b48502"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+ "synstructure",
+]
 
 [[package]]
-name = "windows_x86_64_gnu"
-version = "0.48.5"
+name = "zerotrie"
+version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
+checksum = "2a59c17a5562d507e4b54960e8569ebee33bee890c70aa3fe7b97e85a9fd7851"
+dependencies = [
+ "displaydoc",
+ "yoke",
+ "zerofrom",
+]
 
 [[package]]
-name = "windows_x86_64_gnullvm"
-version = "0.48.5"
+name = "zerovec"
+version = "0.11.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
+checksum = "6c28719294829477f525be0186d13efa9a3c602f7ec202ca9e353d310fb9a002"
+dependencies = [
+ "yoke",
+ "zerofrom",
+ "zerovec-derive",
+]
 
 [[package]]
-name = "windows_x86_64_msvc"
-version = "0.48.5"
+name = "zerovec-derive"
+version = "0.11.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
+checksum = "eadce39539ca5cb3985590102671f2567e659fca9666581ad3411d59207951f3"
+dependencies = [
+ "proc-macro2 1.0.103",
+ "quote 1.0.42",
+ "syn 2.0.111",
+]
diff --git a/Cargo.toml b/Cargo.toml
index bc8393b..16451c0 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -25,21 +25,20 @@ path = "src/main.rs"
 
 [dependencies]
 anyhow = "1.0.41"
-bio = "0.41"
+bio = "3.0.0"
 crossbeam = "0.8"
 crossbeam-channel = "0.5"
 csv = "1.1.6"
-env_logger = "0.9.0"
+env_logger = "0.11.8"
 grep-cli = "0.1.5"
-gzp = "0.10"
-itertools = "0.10.1"
+gzp = "2.0"
+itertools = "0.14.0"
 lazy_static = "1.4.0"
 log = "0.4.11"
 lru_time_cache = "0.11.1"
 num_cpus = "1.13.0"
 rayon = "1.4.0"
-#TODO add  features = ["libdeflate"] when https://github.com/rust-bio/rust-htslib/pull/341 is merged
-rust-htslib = { version = "0.39" }
+rust-htslib = {version = "0.51", default-features = false, features = ["libdeflate"]}
 rust-lapper = "1.0"
 serde = { version = "1.0.116", features = ["derive"] }
 smartstring = { version = "1.0.1", features = ["serde"] }
@@ -49,5 +48,5 @@ termcolor = "1.1.0"
 
 [dev-dependencies]
 proptest = "1.0.0"
-rstest = "0.11.0"
+rstest = "0.26.1"
 tempfile = "3.1.0"
diff --git a/src/commands/base_depth.rs b/src/commands/base_depth.rs
index 03d9461..92daf79 100644
--- a/src/commands/base_depth.rs
+++ b/src/commands/base_depth.rs
@@ -193,6 +193,7 @@ struct BaseProcessor<F: ReadFilter> {
 
 impl<F: ReadFilter> BaseProcessor<F> {
     /// Create a new BaseProcessor
+    #[allow(clippy::too_many_arguments)]
     fn new(
         reads: PathBuf,
         ref_fasta: Option<PathBuf>,
@@ -252,10 +253,7 @@ impl<F: ReadFilter> RegionProcessor for BaseProcessor<F> {
         reader.fetch((tid, start, stop)).expect("Fetched a region");
         // Walk over pileups
         let mut pileup = reader.pileup();
-        pileup.set_max_depth(std::cmp::min(
-            i32::max_value().try_into().unwrap(),
-            self.max_depth,
-        ));
+        pileup.set_max_depth(std::cmp::min(i32::MAX.try_into().unwrap(), self.max_depth));
         let result: Vec<PileupPosition> = pileup
             .flat_map(|p| {
                 let pileup = p.expect("Extracted a pileup");
diff --git a/src/commands/merge_adjacent.rs b/src/commands/merge_adjacent.rs
index d7af29b..0278305 100644
--- a/src/commands/merge_adjacent.rs
+++ b/src/commands/merge_adjacent.rs
@@ -71,7 +71,7 @@ impl MergeAdjacent {
             };
             let mut curr_depth = first.depth;
 
-            while let Some(bedlike) = iter.next() {
+            for bedlike in iter {
                 if bedlike.depth == curr_depth
                     && curr_end >= bedlike.pos
                     && bedlike.ref_seq == curr_seq
diff --git a/src/commands/only_depth.rs b/src/commands/only_depth.rs
index 42ee15d..04d284d 100644
--- a/src/commands/only_depth.rs
+++ b/src/commands/only_depth.rs
@@ -147,7 +147,7 @@ impl OnlyDepth {
             self.bcf_file.clone(),
             !self.skip_merging_intervals,
             Some(cpus),
-            Some(self.chunksize.clone()),
+            Some(self.chunksize),
             Some(self.channel_size_modifier),
             processor,
         );
@@ -205,6 +205,7 @@ struct OnlyDepthProcessor<F: ReadFilter> {
 
 impl<F: ReadFilter> OnlyDepthProcessor<F> {
     /// Create a new OnlyDepthProcessor
+    #[allow(clippy::too_many_arguments)]
     fn new(
         reads: PathBuf,
         ref_fasta: Option<PathBuf>,
@@ -307,7 +308,7 @@ impl<F: ReadFilter> OnlyDepthProcessor<F> {
         for record in reader
             .rc_records()
             .map(|r| r.expect("Read record"))
-            .filter(|read| self.read_filter.filter_read(&read, None))
+            .filter(|read| self.read_filter.filter_read(read, None))
             .flat_map(|record| IterAlignedBlocks::new(record, self.mate_fix))
         {
             let rec_start = u32::try_from(record.0).expect("check overflow");
@@ -396,7 +397,7 @@ impl<F: ReadFilter> OnlyDepthProcessor<F> {
         for record in reader
             .rc_records()
             .map(|r| r.expect("Read record"))
-            .filter(|read| self.read_filter.filter_read(&read, None))
+            .filter(|read| self.read_filter.filter_read(read, None))
         {
             let rec_start = u32::try_from(record.reference_start()).expect("check overflow");
             let rec_stop = u32::try_from(record.reference_end()).expect("check overflow");
diff --git a/src/lib/par_granges.rs b/src/lib/par_granges.rs
index a767abe..613ca3c 100644
--- a/src/lib/par_granges.rs
+++ b/src/lib/par_granges.rs
@@ -87,10 +87,11 @@ impl<R: RegionProcessor + Send + Sync> ParGranges<R> {
     /// * `merge_regions` - If `regions_bed` and or `regions_bcf` is specified, and this is true, merge any overlapping regions to avoid duplicate output.
     /// * `threads`- Optional threads to restrict the number of threads this process will use, defaults to all
     /// * `chunksize`- optional argument to change the default chunksize of 1_000_000. `chunksize` determines the number of bases
-    ///                each worker will get to work on at one time.
+    ///   each worker will get to work on at one time.
     /// * `channel_size_modifier`- Optional argument to modify the default size ration of the channel that `R::P` is sent on.
-    ///                 formula is: ((BYTES_INA_GIGABYTE * channel_size_modifier) * threads) / size_of(R::P)
+    ///   formula is: ((BYTES_INA_GIGABYTE * channel_size_modifier) * threads) / size_of(R::P)
     /// * `processor`- Something that implements [`RegionProcessor`](RegionProcessor)
+    #[allow(clippy::too_many_arguments)]
     pub fn new(
         reads: PathBuf,
         ref_fasta: Option<PathBuf>,
@@ -109,7 +110,7 @@ impl<R: RegionProcessor + Send + Sync> ParGranges<R> {
         };
 
         // Keep two around for main thread and thread running the pool
-        let threads = std::cmp::max(threads.checked_sub(2).unwrap_or(0), 1);
+        let threads = std::cmp::max(threads.saturating_sub(2), 1);
         let pool = rayon::ThreadPoolBuilder::new()
             .num_threads(threads)
             .build()
@@ -198,10 +199,7 @@ impl<R: RegionProcessor + Send + Sync> ParGranges<R> {
                 };
 
                 // The number positions to try to process in one batch
-                let serial_step_size = self
-                    .chunksize
-                    .checked_mul(self.threads as u32)
-                    .unwrap_or(u32::MAX); // aka superchunk
+                let serial_step_size = self.chunksize.saturating_mul(self.threads as u32); // aka superchunk
                 for (tid, intervals) in intervals.into_iter().enumerate() {
                     let tid: u32 = tid as u32;
                     let tid_end: u32 = header.target_len(tid).unwrap().try_into().unwrap();
@@ -210,8 +208,7 @@ impl<R: RegionProcessor + Send + Sync> ParGranges<R> {
                     let mut result = vec![];
                     for chunk_start in (0..tid_end).step_by(serial_step_size as usize) {
                         let tid_name = std::str::from_utf8(header.tid2name(tid)).unwrap();
-                        let chunk_end =
-                            std::cmp::min(chunk_start as u32 + serial_step_size, tid_end);
+                        let chunk_end = std::cmp::min(chunk_start + serial_step_size, tid_end);
                         trace!(
                             "Batch Processing {}:{}-{}",
                             tid_name, chunk_start, chunk_end
@@ -259,15 +256,15 @@ impl<R: RegionProcessor + Send + Sync> ParGranges<R> {
         for tid in 0..(header.target_count()) {
             let tid_len: u32 = header.target_len(tid).unwrap().try_into().unwrap();
             for start in (0..tid_len).step_by(chunksize as usize) {
-                let stop = std::cmp::min(start as u32 + chunksize, tid_len);
+                let stop = std::cmp::min(start + chunksize, tid_len);
                 intervals[tid as usize].push(Interval {
-                    start: start as u32,
-                    stop: stop,
+                    start,
+                    stop,
                     val: (),
                 });
             }
         }
-        Ok(intervals.into_iter().map(|ivs| Lapper::new(ivs)).collect())
+        Ok(intervals.into_iter().map(Lapper::new).collect())
     }
 
     /// Read a bed file into a vector of lappers with the index representing the TID
diff --git a/src/lib/position/pileup_position.rs b/src/lib/position/pileup_position.rs
index 742a7cb..ca59710 100644
--- a/src/lib/position/pileup_position.rs
+++ b/src/lib/position/pileup_position.rs
@@ -107,7 +107,8 @@ impl PileupPosition {
             // Check if we are checking the base quality score
             // && Check if the base quality score is greater or equal to than the cutoff
             if let Some(base_qual_filter) = base_filter
-                && (record.seq().is_empty() || record.qual()[alignment.qpos().unwrap()] < base_qual_filter)
+                && (record.seq().is_empty()
+                    || record.qual()[alignment.qpos().unwrap()] < base_qual_filter)
             {
                 self.n += 1
             } else if let Some(b) = recommended_base {
@@ -222,7 +223,7 @@ impl PileupPosition {
             })
             .sorted_by(|a, b| Ord::cmp(a.1.qname(), b.1.qname()))
             // TODO: I'm not sure there is a good way to remove this allocation
-            .group_by(|a| a.1.qname().to_owned());
+            .chunk_by(|a| a.1.qname().to_owned());
 
         for (_qname, reads) in grouped_by_qname.into_iter() {
             let mut total_reads = 0; // count how many reads there were
@@ -547,11 +548,8 @@ mod tests {
         .unwrap();
 
         // Read with empty SEQ at positions 10-35 - should count toward depth and N count
-        let empty_seq_record = Record::from_sam(
-            &view,
-            b"EMPTY_SEQ\t0\tchr1\t10\t40\t25M\t*\t0\t0\t*\t*",
-        )
-        .unwrap();
+        let empty_seq_record =
+            Record::from_sam(&view, b"EMPTY_SEQ\t0\tchr1\t10\t40\t25M\t*\t0\t0\t*\t*").unwrap();
 
         // Another normal read with 'G' bases at positions 15-40
         let normal_record2 = Record::from_sam(
@@ -584,10 +582,14 @@ mod tests {
         for pileup_result in pileup_iter {
             let pileup = pileup_result.unwrap();
             if pileup.pos() == 14 {
-                let position = PileupPosition::from_pileup(pileup, &header_view, &read_filter, None);
+                let position =
+                    PileupPosition::from_pileup(pileup, &header_view, &read_filter, None);
 
                 // Depth should include all 3 reads
-                assert_eq!(position.depth, 3, "Depth should be 3 (NORMAL + EMPTY_SEQ + NORMAL2)");
+                assert_eq!(
+                    position.depth, 3,
+                    "Depth should be 3 (NORMAL + EMPTY_SEQ + NORMAL2)"
+                );
 
                 // 'A' count from NORMAL read
                 assert_eq!(position.a, 1, "Should have 1 A from NORMAL read");
@@ -629,11 +631,8 @@ mod tests {
         .unwrap();
 
         // Read with empty SEQ
-        let empty_seq_record = Record::from_sam(
-            &view,
-            b"EMPTY_SEQ\t0\tchr1\t1\t40\t25M\t*\t0\t0\t*\t*",
-        )
-        .unwrap();
+        let empty_seq_record =
+            Record::from_sam(&view, b"EMPTY_SEQ\t0\tchr1\t1\t40\t25M\t*\t0\t0\t*\t*").unwrap();
 
         // Write BAM file
         let mut writer = Writer::from_path(&bam_path, &header, bam::Format::Bam).unwrap();
@@ -664,7 +663,10 @@ mod tests {
                 assert_eq!(position.depth, 2, "Depth should be 2");
 
                 // 'A' from NORMAL (quality 'I' = 40, passes filter)
-                assert_eq!(position.a, 1, "Should have 1 A from high-quality NORMAL read");
+                assert_eq!(
+                    position.a, 1,
+                    "Should have 1 A from high-quality NORMAL read"
+                );
 
                 // Empty SEQ read should be counted as N (regardless of base qual filter)
                 assert_eq!(position.n, 1, "Empty SEQ read should be counted as N");
@@ -699,11 +701,8 @@ mod tests {
         .unwrap();
 
         // Read with empty SEQ
-        let empty_seq_record = Record::from_sam(
-            &view,
-            b"EMPTY_SEQ\t0\tchr1\t1\t40\t25M\t*\t0\t0\t*\t*",
-        )
-        .unwrap();
+        let empty_seq_record =
+            Record::from_sam(&view, b"EMPTY_SEQ\t0\tchr1\t1\t40\t25M\t*\t0\t0\t*\t*").unwrap();
 
         // Write BAM file
         let mut writer = Writer::from_path(&bam_path, &header, bam::Format::Bam).unwrap();
diff --git a/src/lib/read_filter.rs b/src/lib/read_filter.rs
index bca1890..c0a6a82 100644
--- a/src/lib/read_filter.rs
+++ b/src/lib/read_filter.rs
@@ -31,8 +31,8 @@ impl ReadFilter for DefaultReadFilter {
     #[inline(always)]
     fn filter_read(&self, read: &Record, _alignment: Option<&Alignment>) -> bool {
         let flags = read.flags();
-        (!flags) & &self.include_flags == 0
-            && flags & &self.exclude_flags == 0
-            && &read.mapq() >= &self.min_mapq
+        (!flags) & self.include_flags == 0
+            && flags & self.exclude_flags == 0
+            && read.mapq() >= self.min_mapq
     }
 }
diff --git a/src/lib/utils.rs b/src/lib/utils.rs
index fbb5f87..58d2f4b 100644
--- a/src/lib/utils.rs
+++ b/src/lib/utils.rs
@@ -29,10 +29,10 @@ pub fn set_rayon_global_pools_size(size: usize) -> Result<()> {
 /// Check if err is a broken pipe.
 #[inline]
 pub fn is_broken_pipe(err: &Error) -> bool {
-    if let Some(io_err) = err.root_cause().downcast_ref::<io::Error>() {
-        if io_err.kind() == io::ErrorKind::BrokenPipe {
-            return true;
-        }
+    if let Some(io_err) = err.root_cause().downcast_ref::<io::Error>()
+        && io_err.kind() == io::ErrorKind::BrokenPipe
+    {
+        return true;
     }
     false
 }