diff --git a/Cargo.lock b/Cargo.lock
index 3e8f1fe..a22e26c 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -3,10 +3,10 @@
 version = 3
 
 [[package]]
-name = "adler"
-version = "1.0.2"
+name = "adler2"
+version = "2.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
+checksum = "512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627"
 
 [[package]]
 name = "aho-corasick"
@@ -19,47 +19,48 @@ dependencies = [
 
 [[package]]
 name = "anstream"
-version = "0.6.13"
+version = "0.6.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb"
+checksum = "64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526"
 dependencies = [
  "anstyle",
  "anstyle-parse",
  "anstyle-query",
  "anstyle-wincon",
  "colorchoice",
+ "is_terminal_polyfill",
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle"
-version = "1.0.6"
+version = "1.0.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc"
+checksum = "1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.3"
+version = "0.2.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c"
+checksum = "eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.0.2"
+version = "1.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648"
+checksum = "6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a"
 dependencies = [
  "windows-sys",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.2"
+version = "3.0.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7"
+checksum = "5bf74e1b6e971609db8ca7a9ce79fd5768ab6ae46441c572e46cf596f59e57f8"
 dependencies = [
  "anstyle",
  "windows-sys",
@@ -67,9 +68,9 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.82"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f538837af36e6f6a9be0faa67f9a314f8119e4e4b5867c6ab40ed60360142519"
+checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da"
 
 [[package]]
 name = "approx"
@@ -80,28 +81,17 @@ dependencies = [
  "num-traits",
 ]
 
-[[package]]
-name = "atty"
-version = "0.2.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
-dependencies = [
- "hermit-abi",
- "libc",
- "winapi",
-]
-
 [[package]]
 name = "autocfg"
-version = "1.2.0"
+version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80"
+checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
 
 [[package]]
 name = "bio"
-version = "1.6.0"
+version = "2.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a72cb93babf08c85b375c2938ac678cc637936b3ebb72266d433cec2577f6c2"
+checksum = "d563b9298d39b3bdb5c45f6e91e0bdcb18d67e6d8fa034a733b7283f2db5ed29"
 dependencies = [
  "anyhow",
  "approx",
@@ -138,9 +128,9 @@ dependencies = [
 
 [[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",
  "lazy_static",
@@ -151,24 +141,24 @@ dependencies = [
 
 [[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 = "buffer-redux"
-version = "1.0.1"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5"
+checksum = "4e8acf87c5b9f5897cd3ebb9a327f420e0cae9dd4e5c1d2e36f2c84c571a58f1"
 dependencies = [
  "memchr",
 ]
@@ -191,9 +181,9 @@ checksum = "5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce"
 
 [[package]]
 name = "bytemuck"
-version = "1.15.0"
+version = "1.17.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d6d68c57235a3a081186990eca2867354726650f42f7516ca50c28d6281fd15"
+checksum = "6fd4c6dcc3b0aea2f5c0b4b82c2b15fe39ddbc76041a310848f4706edf76bb31"
 
 [[package]]
 name = "byteorder"
@@ -203,19 +193,18 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bzip2"
-version = "0.4.4"
+version = "0.5.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8"
+checksum = "75b89e7c29231c673a61a46e722602bcd138298f6b9e81e71119693534585f5c"
 dependencies = [
  "bzip2-sys",
- "libc",
 ]
 
 [[package]]
 name = "bzip2-sys"
-version = "0.1.11+1.0.8"
+version = "0.1.12+1.0.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc"
+checksum = "72ebc2f1a417f01e1da30ef264ee86ae31d2dcd2d603ea283d3c244a883ca2a9"
 dependencies = [
  "cc",
  "libc",
@@ -224,9 +213,12 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.0.94"
+version = "1.2.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "17f6e324229dc011159fcc089755d1e2e216a90d43a7dea6853ca740b84f35e7"
+checksum = "0c3d1b2e905a3a7b00a6141adb0e4c0bb941d11caf55349d863942a1cc44e3c9"
+dependencies = [
+ "shlex",
+]
 
 [[package]]
 name = "cfg-if"
@@ -236,10 +228,9 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
 [[package]]
 name = "chopper"
-version = "0.8.0"
+version = "0.9.1"
 dependencies = [
  "approx",
- "atty",
  "bio",
  "bzip2",
  "clap",
@@ -251,9 +242,9 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.5.4"
+version = "4.5.29"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90bc066a67923782aa8515dbaea16946c5bcc5addbd668bb80af688e53e548a0"
+checksum = "8acebd8ad879283633b343856142139f2da2317c96b05b4dd6181c61e2480184"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -261,9 +252,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.2"
+version = "4.5.29"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4"
+checksum = "f6ba32cbda51c7e1dfd49acc1457ba1a7dec5b64fe360e828acb13ca8dc9c2f9"
 dependencies = [
  "anstream",
  "anstyle",
@@ -273,42 +264,42 @@ dependencies = [
 
 [[package]]
 name = "clap_derive"
-version = "4.5.4"
+version = "4.5.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "528131438037fd55894f62d6e9f068b8f45ac57ffa77517819645d10aed04f64"
+checksum = "bf4ced95c6f4a675af3da73304b9ac4ed991640c36374e4b46795c49e17cf1ed"
 dependencies = [
- "heck 0.5.0",
+ "heck",
  "proc-macro2",
  "quote",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
 name = "clap_lex"
-version = "0.7.0"
+version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce"
+checksum = "f46ad14479a25103f283c0f10005961cf086d8dc42205bb44c46ac563475dca6"
 
 [[package]]
 name = "cmake"
-version = "0.1.50"
+version = "0.1.51"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130"
+checksum = "fb1e43aa7fd152b1f968787f7dbcdeb306d1867ff373c69955211876c053f91a"
 dependencies = [
  "cc",
 ]
 
 [[package]]
 name = "colorchoice"
-version = "1.0.0"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7"
+checksum = "d3fd119d74b830634cea2a0f58bbd0d54540518a14397557951e79340abc28c0"
 
 [[package]]
 name = "crc32fast"
-version = "1.4.0"
+version = "1.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b3855a8a784b474f333699ef2bbca9db2c4a1f6d9088a90a2d25b1eb53111eaa"
+checksum = "a97769d94ddab943e4510d138150169a2758b5ef3eb191a9ee688de3e23ef7b3"
 dependencies = [
  "cfg-if",
 ]
@@ -334,9 +325,9 @@ dependencies = [
 
 [[package]]
 name = "crossbeam-utils"
-version = "0.8.19"
+version = "0.8.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345"
+checksum = "22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80"
 
 [[package]]
 name = "csv"
@@ -367,13 +358,13 @@ checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
 
 [[package]]
 name = "derive-new"
-version = "0.5.9"
+version = "0.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535"
+checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 1.0.109",
+ "syn",
 ]
 
 [[package]]
@@ -384,9 +375,9 @@ checksum = "3e02df23d5b1c6f9e69fa603b890378123b93073df998a21e6e33b9db0a32613"
 
 [[package]]
 name = "either"
-version = "1.11.0"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a47c1c47d2f5964e29c61246e81db715514cd532db6b5116a25ea3c03d6780a2"
+checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0"
 
 [[package]]
 name = "enum-map"
@@ -405,7 +396,7 @@ checksum = "f282cfdfe92516eb26c2af8589c274c7c17681f5ecc03c18255fe741c6aa64eb"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
@@ -428,9 +419,9 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
 [[package]]
 name = "flate2"
-version = "1.0.28"
+version = "1.0.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e"
+checksum = "c936bfdafb507ebbf50b8074c54fa31c5be9a1e7e5f467dd659697041407d07c"
 dependencies = [
  "crc32fast",
  "libz-ng-sys",
@@ -448,9 +439,9 @@ dependencies = [
 
 [[package]]
 name = "getrandom"
-version = "0.2.14"
+version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "94b22e06ecb0110981051723910cbf0b5f5e09a2062dd7663334ee79a9d1286c"
+checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7"
 dependencies = [
  "cfg-if",
  "libc",
@@ -459,15 +450,9 @@ dependencies = [
 
 [[package]]
 name = "hashbrown"
-version = "0.14.3"
+version = "0.14.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604"
-
-[[package]]
-name = "heck"
-version = "0.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
+checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
 
 [[package]]
 name = "heck"
@@ -475,30 +460,27 @@ version = "0.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
-[[package]]
-name = "hermit-abi"
-version = "0.1.19"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33"
-dependencies = [
- "libc",
-]
-
 [[package]]
 name = "indexmap"
-version = "2.2.6"
+version = "2.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26"
+checksum = "93ead53efc7ea8ed3cfb0c79fc8023fbb782a5432b52830b6518941cebe6505c"
 dependencies = [
  "equivalent",
  "hashbrown",
 ]
 
+[[package]]
+name = "is_terminal_polyfill"
+version = "1.70.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf"
+
 [[package]]
 name = "itertools"
-version = "0.11.0"
+version = "0.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57"
+checksum = "413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186"
 dependencies = [
  "either",
 ]
@@ -520,15 +502,15 @@ checksum = "49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b"
 
 [[package]]
 name = "lazy_static"
-version = "1.4.0"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
 name = "libc"
-version = "0.2.153"
+version = "0.2.158"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
+checksum = "d8adc4bb1803a324070e64a98ae98f38934d91957a99cfb3a43dcbc01bc56439"
 
 [[package]]
 name = "libm"
@@ -538,9 +520,9 @@ checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
 [[package]]
 name = "libz-ng-sys"
-version = "1.1.15"
+version = "1.1.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c6409efc61b12687963e602df8ecf70e8ddacf95bc6576bcf16e3ac6328083c5"
+checksum = "7cee1488e961a80d172564fd6fcda11d8a4ac6672c06fe008e9213fa60520c2b"
 dependencies = [
  "cmake",
  "libc",
@@ -548,9 +530,9 @@ dependencies = [
 
 [[package]]
 name = "libz-sys"
-version = "1.1.16"
+version = "1.1.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5e143b5e666b2695d28f6bca6497720813f699c9602dd7f5cac91008b8ada7f9"
+checksum = "fdc53a7799a7496ebc9fd29f31f7df80e83c9bda5299768af5f9e59eeea74647"
 dependencies = [
  "cc",
  "libc",
@@ -571,9 +553,9 @@ dependencies = [
 
 [[package]]
 name = "matrixmultiply"
-version = "0.3.8"
+version = "0.3.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7574c1cf36da4798ab73da5b215bbf444f50718207754cb522201d78d1cd0ff2"
+checksum = "9380b911e3e96d10c1f415da0876389aaf1b56759054eeb0de7df940c456ba1a"
 dependencies = [
  "autocfg",
  "rawpointer",
@@ -581,56 +563,56 @@ dependencies = [
 
 [[package]]
 name = "memchr"
-version = "2.7.2"
+version = "2.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
+checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "minimap2"
-version = "0.1.17+minimap2.2.27"
+version = "0.1.23+minimap2.2.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d920763956405bd0cbeead7e4415097d5780f8a8ce4e1dde0415d15736597dfd"
+checksum = "421be499d25bb88e92934ff5f3400e45505640c3954b1d5c5d825c1ac7cd2c58"
 dependencies = [
  "libc",
  "minimap2-sys",
  "needletail",
- "simdutf8",
 ]
 
 [[package]]
 name = "minimap2-sys"
-version = "0.1.18+minimap2.2.27"
+version = "0.1.21+minimap2.2.28"
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-checksum = "185d3f931e11c1df371455a01e93a0037041d011705b5ff1d283d619b234c47c"
+checksum = "3df64d687208f2ee52e034406c9922313d3e61697d4e8a25da7e7e0b8220bb54"
 dependencies = [
  "cc",
  "libz-sys",
+ "paste",
  "pkg-config",
 ]
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.2"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7"
+checksum = "b3b1c9bd4fe1f0f8b387f6eb9eb3b4a1aa26185e5750efb9140301703f62cd1b"
 dependencies = [
- "adler",
+ "adler2",
 ]
 
 [[package]]
 name = "multimap"
-version = "0.9.1"
+version = "0.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e1a5d38b9b352dbd913288736af36af41c48d61b1a8cd34bcecd727561b7d511"
+checksum = "defc4c55412d89136f966bbb339008b474350e5e6e78d2714439c386b3137a03"
 dependencies = [
  "serde",
 ]
 
 [[package]]
 name = "nalgebra"
-version = "0.29.0"
+version = "0.32.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d506eb7e08d6329505faa8a3a00a5dcc6de9f76e0c77e4b75763ae3c770831ff"
+checksum = "7b5c17de023a86f59ed79891b2e5d5a94c705dbe904a5b5c9c952ea6221b03e4"
 dependencies = [
  "approx",
  "matrixmultiply",
@@ -646,13 +628,13 @@ dependencies = [
 
 [[package]]
 name = "nalgebra-macros"
-version = "0.1.0"
+version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "01fcc0b8149b4632adc89ac3b7b31a12fb6099a0317a4eb2ebff574ef7de7218"
+checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 1.0.109",
+ "syn",
 ]
 
 [[package]]
@@ -670,9 +652,9 @@ dependencies = [
 
 [[package]]
 name = "needletail"
-version = "0.5.1"
+version = "0.6.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "db05a5ab397f64070d8c998fa0fbb84e484b81f95752af317dac183a82d9295d"
+checksum = "de3de09e373770238e3d30eb1a9f09f4754134d0ef354d0570bc1203d2517257"
 dependencies = [
  "buffer-redux",
  "bytecount",
@@ -690,9 +672,9 @@ dependencies = [
 
 [[package]]
 name = "num-complex"
-version = "0.4.5"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "23c6602fda94a57c990fe0df199a035d83576b496aa29f4e634a8ac6004e68a6"
+checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495"
 dependencies = [
  "num-traits",
 ]
@@ -708,20 +690,19 @@ dependencies = [
 
 [[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 = "0.2.18"
+version = "0.2.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da0df0e5185db44f69b44f26786fe401b6c293d1907744beaa7fa62b2e5a517a"
+checksum = "071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841"
 dependencies = [
  "autocfg",
  "libm",
@@ -729,24 +710,24 @@ dependencies = [
 
 [[package]]
 name = "ordered-float"
-version = "3.9.2"
+version = "4.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1e1c390732d15f1d48471625cd92d154e66db2c56645e29a9cd26f4699f72dc"
+checksum = "4a91171844676f8c7990ce64959210cd2eaef32c2612c50f9fae9f8aaa6065a6"
 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 = "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",
@@ -760,15 +741,18 @@ checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec"
 
 [[package]]
 name = "ppv-lite86"
-version = "0.2.17"
+version = "0.2.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
+checksum = "77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04"
+dependencies = [
+ "zerocopy",
+]
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.81"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3d1597b0c024618f09a9c3b8655b7e430397a36d23fdafec26d6965e9eec3eba"
+checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77"
 dependencies = [
  "unicode-ident",
 ]
@@ -850,9 +834,9 @@ dependencies = [
 
 [[package]]
 name = "regex"
-version = "1.10.4"
+version = "1.10.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c"
+checksum = "4219d74c6b67a3654a9fbebc4b419e22126d13d2f3c4a07ee0cb61ff79a79619"
 dependencies = [
  "aho-corasick",
  "memchr",
@@ -862,9 +846,9 @@ dependencies = [
 
 [[package]]
 name = "regex-automata"
-version = "0.4.6"
+version = "0.4.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea"
+checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df"
 dependencies = [
  "aho-corasick",
  "memchr",
@@ -873,9 +857,9 @@ dependencies = [
 
 [[package]]
 name = "regex-syntax"
-version = "0.8.3"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56"
+checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b"
 
 [[package]]
 name = "rustc_version"
@@ -888,21 +872,21 @@ dependencies = [
 
 [[package]]
 name = "rustversion"
-version = "1.0.15"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "80af6f9131f277a45a3fba6ce8e2258037bb0477a67e610d3c1fe046ab31de47"
+checksum = "955d28af4278de8121b7ebeb796b6a45735dc01436d898801014aced2773a3d6"
 
 [[package]]
 name = "ryu"
-version = "1.0.17"
+version = "1.0.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1"
+checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
 
 [[package]]
 name = "safe_arch"
-version = "0.7.1"
+version = "0.7.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f398075ce1e6a179b46f51bd88d0598b92b00d3551f1a2d4ac49e771b56ac354"
+checksum = "c3460605018fdc9612bce72735cba0d27efbcd9904780d44c7e3a9948f96148a"
 dependencies = [
  "bytemuck",
 ]
@@ -915,29 +899,35 @@ checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
 [[package]]
 name = "serde"
-version = "1.0.198"
+version = "1.0.208"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9846a40c979031340571da2545a4e5b7c4163bdae79b301d5f86d03979451fcc"
+checksum = "cff085d2cb684faa248efb494c39b68e522822ac0de72ccf08109abde717cfb2"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.198"
+version = "1.0.208"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e88edab869b01783ba905e7d0153f9fc1a6505a96e4ad3018011eedb838566d9"
+checksum = "24008e81ff7613ed8e5ba0cfaf24e2c2f1e5b8a0495711e44fcd4882fca62bcf"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.60",
+ "syn",
 ]
 
+[[package]]
+name = "shlex"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
+
 [[package]]
 name = "simba"
-version = "0.6.0"
+version = "0.8.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f0b7840f121a46d63066ee7a99fc81dcabbc6105e437cae43528cea199b5a05f"
+checksum = "061507c94fc6ab4ba1c9a0305018408e312e17c041eb63bef8aa726fa33aceae"
 dependencies = [
  "approx",
  "num-complex",
@@ -946,20 +936,13 @@ dependencies = [
  "wide",
 ]
 
-[[package]]
-name = "simdutf8"
-version = "0.1.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a"
-
 [[package]]
 name = "statrs"
-version = "0.16.0"
+version = "0.17.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2d08e5e1748192713cc281da8b16924fb46be7b0c2431854eadc785823e5696e"
+checksum = "f697a07e4606a0a25c044de247e583a330dbb1731d11bc7350b81f48ad567255"
 dependencies = [
  "approx",
- "lazy_static",
  "nalgebra",
  "num-traits",
  "rand",
@@ -973,39 +956,28 @@ checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
 [[package]]
 name = "strum"
-version = "0.25.0"
+version = "0.26.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "290d54ea6f91c969195bdbcd7442c8c2a2ba87da8bf60a7ee86a235d4bc1e125"
+checksum = "8fec0f0aef304996cf250b31b5a10dee7980c85da9d759361292b8bca5a18f06"
 
 [[package]]
 name = "strum_macros"
-version = "0.25.3"
+version = "0.26.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "23dc1fa9ac9c169a78ba62f0b841814b7abae11bdd047b9c58f893439e309ea0"
+checksum = "4c6bee85a5a24955dc440386795aa378cd9cf82acd5f764469152d2270e581be"
 dependencies = [
- "heck 0.4.1",
+ "heck",
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
 name = "syn"
-version = "1.0.109"
+version = "2.0.75"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
-dependencies = [
- "proc-macro2",
- "quote",
- "unicode-ident",
-]
-
-[[package]]
-name = "syn"
-version = "2.0.60"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "909518bc7b1c9b779f1bbf07f2929d35af9f0f37e47c6e9ef7f9dddc1e1821f3"
+checksum = "f6af063034fc1935ede7be0122941bafa9bacb949334d090b77ca98b5817c7d9"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1014,22 +986,22 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.58"
+version = "1.0.63"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "03468839009160513471e86a034bb2c5c0e4baae3b43f79ffc55c4a5427b3297"
+checksum = "c0342370b38b6a11b6cc11d6a805569958d54cfa061a29969c3b5ce2ea405724"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.58"
+version = "1.0.63"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c61f3ba182994efc43764a46c018c347bc492c79f024e705f46567b418f6d4f7"
+checksum = "a4558b58466b9ad7ca0f102865eccc95938dca1a74a856f2b57b6629050da261"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.60",
+ "syn",
 ]
 
 [[package]]
@@ -1052,9 +1024,9 @@ checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
 
 [[package]]
 name = "utf8parse"
-version = "0.2.1"
+version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
+checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
 
 [[package]]
 name = "vcpkg"
@@ -1079,36 +1051,14 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wide"
-version = "0.7.16"
+version = "0.7.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "81a1851a719f11d1d2fea40e15c72f6c00de8c142d7ac47c1441cc7e4d0d5bc6"
+checksum = "b828f995bf1e9622031f8009f8481a85406ce1f4d4588ff746d872043e855690"
 dependencies = [
  "bytemuck",
  "safe_arch",
 ]
 
-[[package]]
-name = "winapi"
-version = "0.3.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
-dependencies = [
- "winapi-i686-pc-windows-gnu",
- "winapi-x86_64-pc-windows-gnu",
-]
-
-[[package]]
-name = "winapi-i686-pc-windows-gnu"
-version = "0.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
-
-[[package]]
-name = "winapi-x86_64-pc-windows-gnu"
-version = "0.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
-
 [[package]]
 name = "windows-sys"
 version = "0.52.0"
@@ -1120,9 +1070,9 @@ dependencies = [
 
 [[package]]
 name = "windows-targets"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb"
+checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
 dependencies = [
  "windows_aarch64_gnullvm",
  "windows_aarch64_msvc",
@@ -1136,51 +1086,51 @@ dependencies = [
 
 [[package]]
 name = "windows_aarch64_gnullvm"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263"
+checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
 
 [[package]]
 name = "windows_aarch64_msvc"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6"
+checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
 
 [[package]]
 name = "windows_i686_gnu"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670"
+checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
 
 [[package]]
 name = "windows_i686_gnullvm"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9"
+checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
 
 [[package]]
 name = "windows_i686_msvc"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf"
+checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
 
 [[package]]
 name = "windows_x86_64_gnu"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9"
+checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596"
+checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
 
 [[package]]
 name = "windows_x86_64_msvc"
-version = "0.52.5"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0"
+checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
 
 [[package]]
 name = "xz2"
@@ -1190,3 +1140,24 @@ checksum = "388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2"
 dependencies = [
  "lzma-sys",
 ]
+
+[[package]]
+name = "zerocopy"
+version = "0.7.35"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0"
+dependencies = [
+ "byteorder",
+ "zerocopy-derive",
+]
+
+[[package]]
+name = "zerocopy-derive"
+version = "0.7.35"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
diff --git a/Cargo.toml b/Cargo.toml
index f268dce..e8c8cb6 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,18 +1,21 @@
 [package]
 name = "chopper"
-version = "0.8.0"
+version = "0.9.1"
 authors = ["wdecoster <decosterwouter@gmail.com>"]
 edition = "2021"
+license = "MIT"
+description = "A tool to filter fastq files"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-bio = "1.3.1"
-clap = { version = "4.2.1", features = ["derive"] }
+bio = "2.0.3"
+clap = { version = "4.5.29", features = ["derive"] }
 rayon = "1.7.0"
 approx = "0.5.1"
-minimap2 = "0.1.17+minimap2.2.27"
-flate2 = { version = "1.0.17", features = ["zlib-ng"], default-features = false }
+minimap2 = "0.1.23+minimap2.2.28"
+flate2 = { version = "1.0.35", features = [
+    "zlib-ng",
+], default-features = false }
 xz2 = "0.1.7"
-bzip2 = "0.4.4"
-atty = "0.2.14"
+bzip2 = "0.5.1"
diff --git a/README.md b/README.md
index a4cc9db..04d6e0c 100644
--- a/README.md
+++ b/README.md
@@ -43,8 +43,6 @@ chopper -q 10 -l 500 -i reads.fastq > filtered_reads.fastq
 chopper -q 10 -l 500 -i reads.fastq.gz | gzip > filtered_reads.fastq.gz
 ```
 
-Note that the tool may be substantially slower in the third example above, and piping while decompressing is recommended (as in the first example). 
-
 ## CITATION
 
 If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/article/39/5/btad311/7160911).
diff --git a/src/main.rs b/src/main.rs
index 581033f..46fae33 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,4 +1,3 @@
-// based on https://docs.rs/bio/0.32.0/bio/io/fastq/index.html#read-and-write
 use bio::io::fastq;
 use clap::Parser;
 use minimap2::*;
@@ -232,20 +231,20 @@ fn ave_qual(quals: &[u8]) -> f64 {
     (probability_sum / quals.len() as f64).log10() * -10.0
 }
 
-fn setup_contamination_filter(contam_fasta: &str, threads: &usize) -> Aligner {
-    Aligner::builder()
+fn setup_contamination_filter(contam_fasta: &str, threads: &usize) -> Arc<Aligner<Built>> {
+    Arc::new(Aligner::builder()
         .preset(Preset::LrHq)
         .with_index_threads(*threads)
         .with_cigar()
         .with_index(contam_fasta, None)
-        .expect("Unable to build index")
+        .expect("Unable to build index"))
 }
 
 // Checks if a sequence is a contaminant, and returns true if so
 // A sequence is considered a contaminant if there is an alignment of at least 90% between query and  target
-fn is_contamination(readseq: &&[u8], contam: &Aligner) -> bool {
+fn is_contamination(readseq: &&[u8], contam: &Arc<Aligner<Built>>) -> bool {
     let alignment = contam
-        .map(readseq, false, false, None, None)
+        .map(readseq, false, false, None, None, None)
         .expect("Unable to align");
     let query_len = readseq.len() as f64;
     if alignment.is_empty() {
diff --git a/src/utils.rs b/src/utils.rs
index dcb1b9f..6800196 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -4,6 +4,8 @@ use std::{
     io::{self, prelude::*, BufRead, BufReader},
     path::Path,
 };
+use std::io::IsTerminal;
+
 
 const MAGIC_MAX_LEN: usize = 6;
 const GZ_MAGIC: [u8; 3] = [0x1f, 0x8b, 0x08];
@@ -85,7 +87,7 @@ where
             Ok(Box::new(BufReader::with_capacity(BUFF_SIZE, fp)))
         }
     } else {
-        if atty::is(atty::Stream::Stdin) {
+        if io::stdin().is_terminal() {
             eprintln!("Error: stdin not detected");
             std::process::exit(1);
         }