diff --git a/Cargo.lock b/Cargo.lock
index 09b2060..d501e9e 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -23,16 +23,16 @@ dependencies = [
 
 [[package]]
 name = "aho-corasick"
-version = "1.1.2"
+version = "1.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0"
+checksum = "8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916"
 dependencies = [
  "memchr",
 ]
 
 [[package]]
 name = "alevin-fry"
-version = "0.8.2"
+version = "0.9.0"
 dependencies = [
  "ahash",
  "anyhow",
@@ -100,47 +100,48 @@ dependencies = [
 
 [[package]]
 name = "anstream"
-version = "0.6.13"
+version = "0.6.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb"
+checksum = "418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b"
 dependencies = [
  "anstyle",
  "anstyle-parse",
  "anstyle-query",
  "anstyle-wincon",
  "colorchoice",
+ "is_terminal_polyfill",
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle"
-version = "1.0.6"
+version = "1.0.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc"
+checksum = "038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.3"
+version = "0.2.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c"
+checksum = "c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.0.2"
+version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648"
+checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391"
 dependencies = [
  "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.2"
+version = "3.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7"
+checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19"
 dependencies = [
  "anstyle",
  "windows-sys 0.52.0",
@@ -148,9 +149,9 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.80"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ad32ce52e4161730f7098c077cd2ed6229b5804ccf99e5366be1ab72a98b4e1"
+checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da"
 
 [[package]]
 name = "approx"
@@ -178,9 +179,9 @@ checksum = "96d30a06541fbafbc7f82ed10c06164cfbd2c401138f6addd8404629c4b16711"
 
 [[package]]
 name = "autocfg"
-version = "1.1.0"
+version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
+checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
 
 [[package]]
 name = "bincode"
@@ -213,15 +214,9 @@ checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
 
 [[package]]
 name = "bitflags"
-version = "1.3.2"
+version = "2.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
-
-[[package]]
-name = "bitflags"
-version = "2.4.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf"
+checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
 
 [[package]]
 name = "block-buffer"
@@ -254,21 +249,21 @@ dependencies = [
 
 [[package]]
 name = "bumpalo"
-version = "3.15.4"
+version = "3.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ff69b9dd49fd426c69a0db9fc04dd934cdb6645ff000864d98f7e2af8830eaa"
+checksum = "79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c"
 
 [[package]]
 name = "bytecount"
-version = "0.6.7"
+version = "0.6.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205"
+checksum = "5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce"
 
 [[package]]
 name = "bytemuck"
-version = "1.14.3"
+version = "1.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a2ef034f05691a48569bd920a96c81b9d91bbad1ab5ac7c4616c1f6ef36cb79f"
+checksum = "b236fc92302c97ed75b38da1f4917b5cdda4984745740f153a5d3059e48d725e"
 
 [[package]]
 name = "byteorder"
@@ -278,9 +273,9 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bytes"
-version = "1.5.0"
+version = "1.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223"
+checksum = "514de17de45fdb8dc022b1a7975556c53c86f9f0aa5f534b98977b171857c2c9"
 
 [[package]]
 name = "bzip2"
@@ -305,9 +300,9 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.0.90"
+version = "1.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8cd6604a82acf3039f1144f54b8eb34e91ffba622051189e71b781822d5ee1f5"
+checksum = "907d8581360765417f8f2e0e7d602733bbed60156b4465b7617243689ef9b83d"
 
 [[package]]
 name = "cfg-if"
@@ -317,23 +312,23 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
 [[package]]
 name = "chrono"
-version = "0.4.35"
+version = "0.4.38"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8eaf5903dcbc0a39312feb77df2ff4c76387d591b9fc7b04a238dcf8bb62639a"
+checksum = "a21f936df1771bf62b77f047b726c4625ff2e8aa607c01ec06e5a05bd8463401"
 dependencies = [
  "android-tzdata",
  "iana-time-zone",
  "js-sys",
  "num-traits",
  "wasm-bindgen",
- "windows-targets 0.52.4",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
 name = "clap"
-version = "4.5.2"
+version = "4.5.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b230ab84b0ffdf890d5a10abdbc8b83ae1c4918275daea1ab8801f71536b2651"
+checksum = "64acc1846d54c1fe936a78dc189c34e28d3f5afc348403f28ecf53660b9b8462"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -341,9 +336,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.2"
+version = "4.5.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4"
+checksum = "6fb8393d67ba2e7bfaf28a23458e4e2b543cc73a99595511eb207fdb8aede942"
 dependencies = [
  "anstream",
  "anstyle",
@@ -354,27 +349,27 @@ dependencies = [
 
 [[package]]
 name = "clap_derive"
-version = "4.5.0"
+version = "4.5.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "307bc0538d5f0f83b8248db3087aa92fe504e4691294d0c96c0eabc33f47ba47"
+checksum = "2bac35c6dafb060fd4d275d9a4ffae97917c13a6327903a8be2153cd964f7085"
 dependencies = [
- "heck",
+ "heck 0.5.0",
  "proc-macro2",
  "quote",
- "syn 2.0.52",
+ "syn 2.0.70",
 ]
 
 [[package]]
 name = "clap_lex"
-version = "0.7.0"
+version = "0.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce"
+checksum = "4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70"
 
 [[package]]
 name = "colorchoice"
-version = "1.0.0"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7"
+checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422"
 
 [[package]]
 name = "console"
@@ -397,18 +392,18 @@ checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f"
 
 [[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",
 ]
 
 [[package]]
 name = "crossbeam-channel"
-version = "0.5.12"
+version = "0.5.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ab3db02a9c5b5121e1e42fbdb1aeb65f5e02624cc58c43f2884c6ccac0b82f95"
+checksum = "33480d6946193aa8033910124896ca395333cae7e2d1113d1fef6c3272217df2"
 dependencies = [
  "crossbeam-utils",
 ]
@@ -443,9 +438,9 @@ 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 = "crypto-common"
@@ -480,11 +475,12 @@ dependencies = [
 
 [[package]]
 name = "dashmap"
-version = "5.5.3"
+version = "6.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "978747c1d849a7d2ee5e8adc0159961c48fb7e5db2f06af6723b80123bb53856"
+checksum = "804c8821570c3f8b70230c2ba75ffa5c0f9a4189b9a432b6656c536712acae28"
 dependencies = [
  "cfg-if",
+ "crossbeam-utils",
  "hashbrown",
  "lock_api",
  "once_cell",
@@ -500,6 +496,17 @@ dependencies = [
  "powerfmt",
 ]
 
+[[package]]
+name = "derivative"
+version = "2.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fcc3dd5e9e9c0b295d6e1e4d811fb6f157d5ffd784b8d202fc62eac8035a770b"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 1.0.109",
+]
+
 [[package]]
 name = "derive-new"
 version = "0.5.9"
@@ -544,9 +551,9 @@ dependencies = [
 
 [[package]]
 name = "either"
-version = "1.10.0"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "11157ac094ffbdde99aa67b23417ebdd801842852b500e395a45a9c0aac03e4a"
+checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0"
 
 [[package]]
 name = "encode_unicode"
@@ -562,9 +569,9 @@ checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
 
 [[package]]
 name = "errno"
-version = "0.3.8"
+version = "0.3.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a258e46cdc063eb8519c00b9fc845fc47bcfca4130e2f08e88665ceda8474245"
+checksum = "534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba"
 dependencies = [
  "libc",
  "windows-sys 0.52.0",
@@ -578,9 +585,9 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
 [[package]]
 name = "flate2"
-version = "1.0.28"
+version = "1.0.30"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e"
+checksum = "5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae"
 dependencies = [
  "crc32fast",
  "miniz_oxide",
@@ -598,9 +605,9 @@ dependencies = [
 
 [[package]]
 name = "getrandom"
-version = "0.2.12"
+version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "190092ea657667030ac6a35e305e62fc4dd69fd98ac98631e5d3a2b1575a12b5"
+checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7"
 dependencies = [
  "cfg-if",
  "libc",
@@ -609,9 +616,9 @@ dependencies = [
 
 [[package]]
 name = "hashbrown"
-version = "0.14.3"
+version = "0.14.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604"
+checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
 
 [[package]]
 name = "heck"
@@ -619,6 +626,12 @@ version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
+[[package]]
+name = "heck"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
+
 [[package]]
 name = "hermit-abi"
 version = "0.3.9"
@@ -650,9 +663,9 @@ dependencies = [
 
 [[package]]
 name = "indexmap"
-version = "2.2.5"
+version = "2.2.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b0b929d511467233429c45a44ac1dcaa21ba0f5ba11e4879e6ed28ddb4f9df4"
+checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26"
 dependencies = [
  "equivalent",
  "hashbrown",
@@ -673,9 +686,9 @@ dependencies = [
 
 [[package]]
 name = "instant"
-version = "0.1.12"
+version = "0.1.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c"
+checksum = "e0242819d153cba4b4b05a5a8f2a7e9bbf97b6055b2a002b395c96b5ff3c0222"
 dependencies = [
  "cfg-if",
 ]
@@ -691,20 +704,26 @@ dependencies = [
  "windows-sys 0.52.0",
 ]
 
+[[package]]
+name = "is_terminal_polyfill"
+version = "1.70.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800"
+
 [[package]]
 name = "itertools"
-version = "0.12.1"
+version = "0.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569"
+checksum = "413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186"
 dependencies = [
  "either",
 ]
 
 [[package]]
 name = "itoa"
-version = "1.0.10"
+version = "1.0.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c"
+checksum = "49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b"
 
 [[package]]
 name = "js-sys"
@@ -717,9 +736,9 @@ dependencies = [
 
 [[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 = "lexical-core"
@@ -787,9 +806,9 @@ dependencies = [
 
 [[package]]
 name = "libc"
-version = "0.2.153"
+version = "0.2.155"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
+checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c"
 
 [[package]]
 name = "libm"
@@ -799,9 +818,9 @@ checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
 [[package]]
 name = "libmimalloc-sys"
-version = "0.1.35"
+version = "0.1.39"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3979b5c37ece694f1f5e51e7ecc871fdb0f517ed04ee45f88d15d6d553cb9664"
+checksum = "23aa6811d3bd4deb8a84dde645f943476d13b248d818edcf8ce0b2f37f036b44"
 dependencies = [
  "cc",
  "libc",
@@ -809,13 +828,17 @@ dependencies = [
 
 [[package]]
 name = "libradicl"
-version = "0.8.2"
-source = "git+https://github.com/COMBINE-lab/libradicl?branch=develop#d10845e2a96f4eaf0a14f8aee136bdc0c8330acb"
+version = "0.9.0"
+source = "git+https://github.com/COMBINE-lab/libradicl?branch=develop#96a7c7a59a833d664fa86b9e9a517d021d1df844"
 dependencies = [
  "ahash",
  "anyhow",
  "bio-types",
+ "bytemuck",
+ "crossbeam-queue",
  "dashmap",
+ "derivative",
+ "itertools",
  "noodles-bam",
  "noodles-sam",
  "num",
@@ -827,26 +850,25 @@ dependencies = [
 
 [[package]]
 name = "libredox"
-version = "0.0.1"
+version = "0.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "85c833ca1e66078851dba29046874e38f08b2c883700aa29a03ddd3b23814ee8"
+checksum = "c0ff37bd590ca25063e35af745c343cb7a0271906fb7b37e4813e8f79f00268d"
 dependencies = [
- "bitflags 2.4.2",
+ "bitflags",
  "libc",
- "redox_syscall",
 ]
 
 [[package]]
 name = "linux-raw-sys"
-version = "0.4.13"
+version = "0.4.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "01cda141df6706de531b6c46c3a33ecca755538219bd484262fa09410c13539c"
+checksum = "78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89"
 
 [[package]]
 name = "lock_api"
-version = "0.4.11"
+version = "0.4.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
+checksum = "07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17"
 dependencies = [
  "autocfg",
  "scopeguard",
@@ -854,9 +876,9 @@ dependencies = [
 
 [[package]]
 name = "log"
-version = "0.4.21"
+version = "0.4.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
+checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
 
 [[package]]
 name = "lzma-sys"
@@ -891,38 +913,38 @@ dependencies = [
 
 [[package]]
 name = "memchr"
-version = "2.7.1"
+version = "2.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "523dc4f511e55ab87b694dc30d0f820d60906ef06413f93d4d7a1385599cc149"
+checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "mimalloc"
-version = "0.1.39"
+version = "0.1.43"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fa01922b5ea280a911e323e4d2fd24b7fe5cc4042e0d2cda3c40775cdc4bdc9c"
+checksum = "68914350ae34959d83f732418d51e2427a794055d0b9529f48259ac07af65633"
 dependencies = [
  "libmimalloc-sys",
 ]
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.2"
+version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7"
+checksum = "b8a240ddb74feaf34a79a7add65a741f3167852fba007066dcac1ca548d89c08"
 dependencies = [
  "adler",
 ]
 
 [[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 0.5.1",
  "matrixmultiply",
  "nalgebra-macros",
- "num-complex 0.4.5",
+ "num-complex 0.4.6",
  "num-rational",
  "num-traits",
  "rand",
@@ -933,13 +955,13 @@ 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 2.0.70",
 ]
 
 [[package]]
@@ -949,7 +971,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32"
 dependencies = [
  "matrixmultiply",
- "num-complex 0.4.5",
+ "num-complex 0.4.6",
  "num-integer",
  "num-traits",
  "rawpointer",
@@ -971,9 +993,9 @@ dependencies = [
 
 [[package]]
 name = "noodles"
-version = "0.65.0"
+version = "0.77.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "38db1833ba39368f7a855c5b9a8412729a61dd86b2563e1a3bdb02aecbe92a3c"
+checksum = "6f8629ce12eeb2d6483be18af64beb9488840299ecd617be4ec2f4ebf66688e6"
 dependencies = [
  "noodles-bam",
  "noodles-bgzf",
@@ -982,9 +1004,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-bam"
-version = "0.56.0"
+version = "0.64.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d3189e8ecee801ab5c3f4ea9908c4196b429137d8d35d733f00f6681f9188be7"
+checksum = "3fd4e9825cce4ed3c7fa958efce37268d899bdb7fdeb22d73493a095de1564be"
 dependencies = [
  "bit-vec",
  "bstr",
@@ -999,9 +1021,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-bgzf"
-version = "0.26.0"
+version = "0.31.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8970db2e84adb1007377dd3988258d7a64e3fc4c05602ebf94e1f8cba207c030"
+checksum = "754f4d28655c5d486e2a62814c5dcc46ad2cee5a2b6cbe91fd765a5ec997f91a"
 dependencies = [
  "byteorder",
  "bytes",
@@ -1011,17 +1033,20 @@ dependencies = [
 
 [[package]]
 name = "noodles-core"
-version = "0.14.0"
+version = "0.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7336c3be652de4e05444c9b12a32331beb5ba3316e8872d92bfdd8ef3b06c282"
+checksum = "c5a8c6b020d1205abef2b0fab4463a6c5ecc3c8f4d561ca8b0d1a42323376200"
+dependencies = [
+ "bstr",
+]
 
 [[package]]
 name = "noodles-cram"
-version = "0.56.0"
+version = "0.65.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "34a70ebb5bc7ff2d07ce96c0568691e57be421c121103ebef10cf02a63d7d400"
+checksum = "4cf95f7e286f62550121f6135a1cb372a0233eba7bffb7f7bebe55eb4f12b35c"
 dependencies = [
- "bitflags 2.4.2",
+ "bitflags",
  "bstr",
  "byteorder",
  "bytes",
@@ -1038,9 +1063,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-csi"
-version = "0.30.0"
+version = "0.36.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a60dfe0919f7ecbd081a82eb1d32e8f89f9041932d035fe8309073c8c01277bf"
+checksum = "89ac24bac459ae99c046086d771f5a79f632ab27a9280406f2fbb7a3238d79cc"
 dependencies = [
  "bit-vec",
  "byteorder",
@@ -1051,10 +1076,11 @@ dependencies = [
 
 [[package]]
 name = "noodles-fasta"
-version = "0.33.0"
+version = "0.40.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5e9e953e4e90e6c96e6a384598ebf2ab6d2f5add259ff05a194cf635e892c980"
+checksum = "195e5a37b273b03499d85a83e9101532c02a21c7b9b2d9c11960b6fbfdcd39ad"
 dependencies = [
+ "bstr",
  "bytes",
  "memchr",
  "noodles-bgzf",
@@ -1063,11 +1089,11 @@ dependencies = [
 
 [[package]]
 name = "noodles-sam"
-version = "0.53.0"
+version = "0.61.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1f0d8e441368374f6e144989f823fd7c05e58cdaa3f97d22bb4d75b534327b87"
+checksum = "48e2636562b1b13e21369e82b0426cd532a3fb2dc676eccec89215a1a8dad243"
 dependencies = [
- "bitflags 2.4.2",
+ "bitflags",
  "bstr",
  "indexmap",
  "lexical-core",
@@ -1079,9 +1105,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-util"
-version = "0.37.0"
+version = "0.48.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e800d2619f75de004aef8beb29f604e667f5bf5f714ff05cce3730f5c8cc4958"
+checksum = "b2aa80a65a665b668318834f00b5e84286ef3ca59a702b11de4cb3e8f2564c91"
 dependencies = [
  "flate2",
  "noodles-bam",
@@ -1095,12 +1121,12 @@ dependencies = [
 
 [[package]]
 name = "num"
-version = "0.4.1"
+version = "0.4.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b05180d69e3da0e530ba2a1dae5110317e49e3b7f3d41be227dc5f92e49ee7af"
+checksum = "35bd024e8b2ff75562e5f34e7f4905839deb4b22955ef5e73d2fea1b9813cb23"
 dependencies = [
  "num-bigint",
- "num-complex 0.4.5",
+ "num-complex 0.4.6",
  "num-integer",
  "num-iter",
  "num-rational",
@@ -1109,11 +1135,10 @@ dependencies = [
 
 [[package]]
 name = "num-bigint"
-version = "0.4.4"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "608e7659b5c3d7cba262d894801b9ec9d00de989e8a82bd4bef91d08da45cdc0"
+checksum = "a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9"
 dependencies = [
- "autocfg",
  "num-integer",
  "num-traits",
 ]
@@ -1130,9 +1155,9 @@ 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",
 ]
@@ -1164,9 +1189,9 @@ dependencies = [
 
 [[package]]
 name = "num-iter"
-version = "0.1.44"
+version = "0.1.45"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d869c01cc0c455284163fd0092f1f93835385ccab5a98a0dcc497b2f8bf055a9"
+checksum = "1429034a0490724d0075ebb2bc9e875d6503c3cf69e235a8941aa757d83ef5bf"
 dependencies = [
  "autocfg",
  "num-integer",
@@ -1175,11 +1200,10 @@ 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-bigint",
  "num-integer",
  "num-traits",
@@ -1187,9 +1211,9 @@ dependencies = [
 
 [[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",
@@ -1219,28 +1243,28 @@ checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
 
 [[package]]
 name = "parking_lot_core"
-version = "0.9.9"
+version = "0.9.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e"
+checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
 dependencies = [
  "cfg-if",
  "libc",
  "redox_syscall",
  "smallvec",
- "windows-targets 0.48.5",
+ "windows-targets 0.52.6",
 ]
 
 [[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",
@@ -1272,18 +1296,18 @@ checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.78"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2422ad645d89c99f8f3e6b88a9fdeca7fabeac836b1002371c4367c8f984aae"
+checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77"
 dependencies = [
  "unicode-ident",
 ]
 
 [[package]]
 name = "quote"
-version = "1.0.35"
+version = "1.0.36"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef"
+checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
 dependencies = [
  "proc-macro2",
 ]
@@ -1336,9 +1360,9 @@ checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
 
 [[package]]
 name = "rayon"
-version = "1.9.0"
+version = "1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e4963ed1bc86e4f3ee217022bd855b297cef07fb9eac5dfa1f788b220b49b3bd"
+checksum = "b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa"
 dependencies = [
  "either",
  "rayon-core",
@@ -1356,18 +1380,18 @@ dependencies = [
 
 [[package]]
 name = "redox_syscall"
-version = "0.4.1"
+version = "0.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
+checksum = "c82cf8cff14456045f55ec4241383baeff27af886adb72ffb2162f99911de0fd"
 dependencies = [
- "bitflags 1.3.2",
+ "bitflags",
 ]
 
 [[package]]
 name = "redox_users"
-version = "0.4.4"
+version = "0.4.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a18479200779601e498ada4e8c1e1f50e3ee19deb0259c25825a98b5603b2cb4"
+checksum = "bd283d9651eeda4b2a83a43c1c91b266c40fd76ecd39a50a8c630ae69dc72891"
 dependencies = [
  "getrandom",
  "libredox",
@@ -1376,9 +1400,9 @@ dependencies = [
 
 [[package]]
 name = "regex"
-version = "1.10.3"
+version = "1.10.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b62dbe01f0b06f9d8dc7d49e05a0785f153b00b2c227856282f671e0318c9b15"
+checksum = "b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f"
 dependencies = [
  "aho-corasick",
  "memchr",
@@ -1388,9 +1412,9 @@ 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",
@@ -1399,17 +1423,17 @@ dependencies = [
 
 [[package]]
 name = "regex-syntax"
-version = "0.8.2"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f"
+checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b"
 
 [[package]]
 name = "rustix"
-version = "0.38.31"
+version = "0.38.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6ea3e1a662af26cd7a3ba09c0297a31af215563ecf42817c98df621387f4e949"
+checksum = "70dc5ec042f7a43c4a73241207cecc9873a06d45debb38b329f8541d85c2730f"
 dependencies = [
- "bitflags 2.4.2",
+ "bitflags",
  "errno",
  "libc",
  "linux-raw-sys",
@@ -1418,21 +1442,21 @@ dependencies = [
 
 [[package]]
 name = "rustversion"
-version = "1.0.14"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4"
+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",
 ]
@@ -1465,29 +1489,29 @@ checksum = "6ab8598aa408498679922eff7fa985c25d58a90771bd6be794434c5277eab1a6"
 
 [[package]]
 name = "serde"
-version = "1.0.197"
+version = "1.0.204"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2"
+checksum = "bc76f558e0cbb2a839d37354c575f1dc3fdc6546b5be373ba43d95f231bf7c12"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.197"
+version = "1.0.204"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b"
+checksum = "e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.52",
+ "syn 2.0.70",
 ]
 
 [[package]]
 name = "serde_json"
-version = "1.0.114"
+version = "1.0.120"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c5f09b1bd632ef549eaa9f60a1f8de742bdbc698e6cee2095fc84dde5f549ae0"
+checksum = "4e0d21c9a8cae1235ad58a00c11cb40d4b1e5c784f1ef2c537876ed6ffd8b7c5"
 dependencies = [
  "itoa",
  "ryu",
@@ -1496,12 +1520,12 @@ dependencies = [
 
 [[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 0.5.1",
- "num-complex 0.4.5",
+ "num-complex 0.4.6",
  "num-traits",
  "paste",
  "wide",
@@ -1540,9 +1564,9 @@ dependencies = [
 
 [[package]]
 name = "smallvec"
-version = "1.13.1"
+version = "1.13.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7"
+checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
 
 [[package]]
 name = "snap"
@@ -1558,7 +1582,7 @@ checksum = "88bab60b0a18fb9b3e0c26e92796b3c3a278bf5fa4880f5ad5cc3bdfb843d0b1"
 dependencies = [
  "alga",
  "ndarray",
- "num-complex 0.4.5",
+ "num-complex 0.4.6",
  "num-traits",
  "num_cpus",
  "rayon",
@@ -1573,12 +1597,11 @@ checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
 
 [[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 0.5.1",
- "lazy_static",
  "nalgebra",
  "num-traits",
  "rand",
@@ -1586,9 +1609,9 @@ dependencies = [
 
 [[package]]
 name = "strsim"
-version = "0.11.0"
+version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ee073c9e4cd00e28217186dbe12796d692868f432bf2e97ee73bed0c56dfa01"
+checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
 [[package]]
 name = "strum_macros"
@@ -1596,11 +1619,11 @@ version = "0.25.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "23dc1fa9ac9c169a78ba62f0b841814b7abae11bdd047b9c58f893439e309ea0"
 dependencies = [
- "heck",
+ "heck 0.4.1",
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.52",
+ "syn 2.0.70",
 ]
 
 [[package]]
@@ -1616,9 +1639,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.52"
+version = "2.0.70"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b699d15b36d1f02c3e7c69f8ffef53de37aefae075d8488d4ba1a7788d574a07"
+checksum = "2f0209b68b3613b093e0ec905354eccaedcfe83b8cb37cbdeae64026c3064c16"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1654,22 +1677,22 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.57"
+version = "1.0.62"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1e45bcbe8ed29775f228095caf2cd67af7a4ccf756ebff23a306bf3e8b47b24b"
+checksum = "f2675633b1499176c2dff06b0856a27976a8f9d436737b4cf4f312d4d91d8bbb"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.57"
+version = "1.0.62"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a953cb265bef375dae3de6663da4d3804eee9682ea80d8e2542529b73c531c81"
+checksum = "d20468752b09f49e909e55a5d338caa8bedf615594e9d80bc4c565d30faf798c"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.52",
+ "syn 2.0.70",
 ]
 
 [[package]]
@@ -1684,9 +1707,9 @@ dependencies = [
 
 [[package]]
 name = "time"
-version = "0.3.34"
+version = "0.3.36"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c8248b6521bb14bc45b4067159b9b6ad792e2d6d754d6c41fb50e29fefe38749"
+checksum = "5dfd88e563464686c916c7e46e623e520ddc6d79fa6641390f2e3fa86e83e885"
 dependencies = [
  "deranged",
  "itoa",
@@ -1705,9 +1728,9 @@ checksum = "ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3"
 
 [[package]]
 name = "time-macros"
-version = "0.2.17"
+version = "0.2.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ba3a3ef41e6672a2f0f001392bb5dcd3ff0a9992d618ca761a11c3121547774"
+checksum = "3f252a68540fde3a3877aeea552b832b40ab9a69e318efd078774a01ddee1ccf"
 dependencies = [
  "num-conv",
  "time-core",
@@ -1726,22 +1749,22 @@ dependencies = [
 
 [[package]]
 name = "typed-builder"
-version = "0.18.1"
+version = "0.18.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "444d8748011b93cb168770e8092458cb0f8854f931ff82fdf6ddfbd72a9c933e"
+checksum = "77739c880e00693faef3d65ea3aad725f196da38b22fdc7ea6ded6e1ce4d3add"
 dependencies = [
  "typed-builder-macro",
 ]
 
 [[package]]
 name = "typed-builder-macro"
-version = "0.18.1"
+version = "0.18.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "563b3b88238ec95680aef36bdece66896eaa7ce3c0f1b4f39d38fb2435261352"
+checksum = "1f718dfaf347dcb5b983bfc87608144b0bad87970aebcbea5ce44d2a30c08e63"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.52",
+ "syn 2.0.70",
 ]
 
 [[package]]
@@ -1758,15 +1781,15 @@ checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
 
 [[package]]
 name = "unicode-width"
-version = "0.1.11"
+version = "0.1.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e51733f11c9c4f72aa0c160008246859e340b00807569a0da0e7a1079b27ba85"
+checksum = "0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d"
 
 [[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 = "version_check"
@@ -1801,7 +1824,7 @@ dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.52",
+ "syn 2.0.70",
  "wasm-bindgen-shared",
 ]
 
@@ -1823,7 +1846,7 @@ checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.52",
+ "syn 2.0.70",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
@@ -1836,9 +1859,9 @@ checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96"
 
 [[package]]
 name = "wide"
-version = "0.7.15"
+version = "0.7.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "89beec544f246e679fc25490e3f8e08003bc4bf612068f325120dad4cea02c1c"
+checksum = "2caba658a80831539b30698ae9862a72db6697dfdd7151e46920f5f2755c3ce2"
 dependencies = [
  "bytemuck",
  "safe_arch",
@@ -1872,7 +1895,7 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
 dependencies = [
- "windows-targets 0.52.4",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -1890,7 +1913,7 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
 dependencies = [
- "windows-targets 0.52.4",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -1910,17 +1933,18 @@ dependencies = [
 
 [[package]]
 name = "windows-targets"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7dd37b7e5ab9018759f893a1952c9420d060016fc19a472b4bb20d1bdd694d1b"
+checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
 dependencies = [
- "windows_aarch64_gnullvm 0.52.4",
- "windows_aarch64_msvc 0.52.4",
- "windows_i686_gnu 0.52.4",
- "windows_i686_msvc 0.52.4",
- "windows_x86_64_gnu 0.52.4",
- "windows_x86_64_gnullvm 0.52.4",
- "windows_x86_64_msvc 0.52.4",
+ "windows_aarch64_gnullvm 0.52.6",
+ "windows_aarch64_msvc 0.52.6",
+ "windows_i686_gnu 0.52.6",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc 0.52.6",
+ "windows_x86_64_gnu 0.52.6",
+ "windows_x86_64_gnullvm 0.52.6",
+ "windows_x86_64_msvc 0.52.6",
 ]
 
 [[package]]
@@ -1931,9 +1955,9 @@ checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
 
 [[package]]
 name = "windows_aarch64_gnullvm"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bcf46cf4c365c6f2d1cc93ce535f2c8b244591df96ceee75d8e83deb70a9cac9"
+checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
 
 [[package]]
 name = "windows_aarch64_msvc"
@@ -1943,9 +1967,9 @@ checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
 
 [[package]]
 name = "windows_aarch64_msvc"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da9f259dd3bcf6990b55bffd094c4f7235817ba4ceebde8e6d11cd0c5633b675"
+checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
 
 [[package]]
 name = "windows_i686_gnu"
@@ -1955,9 +1979,15 @@ checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
 
 [[package]]
 name = "windows_i686_gnu"
-version = "0.52.4"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
+
+[[package]]
+name = "windows_i686_gnullvm"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3"
+checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
 
 [[package]]
 name = "windows_i686_msvc"
@@ -1967,9 +1997,9 @@ checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
 
 [[package]]
 name = "windows_i686_msvc"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02"
+checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
 
 [[package]]
 name = "windows_x86_64_gnu"
@@ -1979,9 +2009,9 @@ checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
 
 [[package]]
 name = "windows_x86_64_gnu"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03"
+checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
@@ -1991,9 +2021,9 @@ checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177"
+checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
 
 [[package]]
 name = "windows_x86_64_msvc"
@@ -2003,9 +2033,9 @@ checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
 
 [[package]]
 name = "windows_x86_64_msvc"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8"
+checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
 
 [[package]]
 name = "xz2"
@@ -2018,20 +2048,20 @@ dependencies = [
 
 [[package]]
 name = "zerocopy"
-version = "0.7.32"
+version = "0.7.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be"
+checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0"
 dependencies = [
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.7.32"
+version = "0.7.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6"
+checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.52",
+ "syn 2.0.70",
 ]
diff --git a/Cargo.toml b/Cargo.toml
index eeefa95..694b7ae 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -35,46 +35,46 @@ categories = ["command-line-utilities", "science"]
 [dependencies]
 # for local development, look in the libradicl git repository
 # but when published, pull the specified version
-libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.8.2" }
-anyhow = "1.0.80"
+libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.9.0" }
+anyhow = "1.0.86"
 arrayvec = "0.7.4"
 ahash = "0.8.11"
 bincode = "1.3.3"
 bstr = "1.9.1"
-crossbeam-channel = "0.5.12"
+crossbeam-channel = "0.5.13"
 crossbeam-queue = "0.3.11"
-typed-builder = "0.18.1"
+typed-builder = "0.18.2"
 indicatif = "0.17.8"
 needletail = "0.5.1"
-petgraph = "0.6.4"
-flate2 = "1.0.28"
+petgraph = "0.6.5"
+flate2 = "1.0.30"
 scroll = "0.12.0"
-serde = { version = "1.0.197", features = ["derive"] }
-serde_json = "1.0.114"
+serde = { version = "1.0.204", features = ["derive"] }
+serde_json = "1.0.120"
 sprs = "0.11.1"
 slog = "2.7.0"
 slog-term = "2.9.1"
 slog-async = "2.8.0"
-smallvec = "1.13.1"
+smallvec = "1.13.2"
 snap = "1.1.1"
 rand = "0.8.5"
-chrono = "0.4.35"
+chrono = "0.4.38"
 csv = "1.3.0"
-mimalloc = { version = "0.1.39", default-features = false }
+mimalloc = { version = "0.1.43", default-features = false }
 num-format = "0.4.4"
 num_cpus = "1.16.0"
 bio-types = { version = "1.0.1", default-features = true, features = ["serde"] }
-itertools = "0.12.1"
-thiserror = "1.0.57"
-statrs = "0.16.0"
+itertools = "0.13.0"
+thiserror = "1.0.61"
+statrs = "0.17.1"
 sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "dev", version = "0.2.0" }
 
 # no shenanigans; clap makes breaking "fixes" too often to allow variability
 # in the version different from what we tested with
-clap = { version = "=4.5.2", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] }
+clap = { version = "4.5.9", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] }
 
-noodles = { version = "0.65.0", features = ["bam", "bgzf", "sam"] }
-noodles-util = { version = "0.37.0", features = ["alignment"] }
+noodles = { version = "0.77.0", features = ["bam", "bgzf", "sam"] }
+noodles-util = { version = "0.48.0", features = ["alignment"] }
 
 [profile.release]
 #debug = true
diff --git a/src/collate.rs b/src/collate.rs
index d296fd1..ccbe2a9 100644
--- a/src/collate.rs
+++ b/src/collate.rs
@@ -466,7 +466,7 @@ where
         correct_map.len().to_formatted_string(&Locale::en)
     );
 
-    let cc = chunk::ChunkConfig {
+    let cc = chunk::AlevinFryChunkContext {
         num_chunks: hdr.num_chunks,
         bc_type: libradicl::rad_types::encode_type_tag(bct).expect("valid barcode tag type"),
         umi_type: libradicl::rad_types::encode_type_tag(umit).expect("valid umi tag type"),
diff --git a/src/convert.rs b/src/convert.rs
index 4247f7d..423ab56 100644
--- a/src/convert.rs
+++ b/src/convert.rs
@@ -108,6 +108,9 @@ fn write_barcode<W: Write>(barcode_t: &RadType, barcode: u64, w: &mut W) -> anyh
                 let v = barcode;
                 w.write_all(&v.to_le_bytes())?;
             }
+            RadIntId::U128 => {
+                todo!("support for u128-encoded barcodes is not yet available");
+            }
         },
         _ => bail!("invalid type!"),
     }
diff --git a/src/io_utils.rs b/src/io_utils.rs
index 5c6a1a3..a84a2af 100644
--- a/src/io_utils.rs
+++ b/src/io_utils.rs
@@ -7,7 +7,7 @@
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
 
-/// some (hopefully) generally useful I/O related utilities
+/*
 use anyhow::Context;
 use crossbeam_queue::ArrayQueue;
 use indicatif::ProgressBar;
@@ -87,10 +87,10 @@ pub(crate) fn fill_work_queue<T: Read>(
 
         // determine if we should dump the current buffer to the work queue
         if force_push  // if we were told to push this chunk
-	    || // or if adding the next cell to this chunk would exceed the buffer size
-	    ((cbytes + nbytes_chunk) as usize > buf.len() && cells_in_chunk > 0)
-	    || // of if this was the last chunk
-	    chunk_num == num_chunks
+        || // or if adding the next cell to this chunk would exceed the buffer size
+        ((cbytes + nbytes_chunk) as usize > buf.len() && cells_in_chunk > 0)
+        || // of if this was the last chunk
+        chunk_num == num_chunks
         {
             // launch off these cells on the queue
             let mut bclone = (first_cell, cells_in_chunk, cbytes, crec, buf.clone());
@@ -196,10 +196,10 @@ pub(crate) fn fill_work_queue_filtered<T: Read>(
 
         // determine if we should dump the current buffer to the work queue
         if force_push  // if we were told to push this chunk
-	    || // or if adding the next cell to this chunk would exceed the buffer size
-	    ((cbytes + nbytes_chunk) as usize > buf.len() && cells_in_chunk > 0)
-	    || // of if this was the last chunk
-	    chunk_num == num_chunks
+        || // or if adding the next cell to this chunk would exceed the buffer size
+        ((cbytes + nbytes_chunk) as usize > buf.len() && cells_in_chunk > 0)
+        || // of if this was the last chunk
+        chunk_num == num_chunks
         {
             // launch off these cells on the queue
             let mut bclone = (first_cell, cells_in_chunk, cbytes, crec, buf.clone());
@@ -223,3 +223,4 @@ pub(crate) fn fill_work_queue_filtered<T: Read>(
     }
     Ok(())
 }
+*/
diff --git a/src/quant.rs b/src/quant.rs
index 3d2222f..126f431 100644
--- a/src/quant.rs
+++ b/src/quant.rs
@@ -8,7 +8,6 @@
  */
 
 use anyhow::Context;
-use crossbeam_queue::ArrayQueue;
 use indicatif::{ProgressBar, ProgressDrawTarget, ProgressStyle};
 
 #[allow(unused_imports)]
@@ -16,15 +15,13 @@ use slog::{crit, info, warn};
 
 use needletail::bitkmer::*;
 use num_format::{Locale, ToFormattedString};
-use scroll::Pread;
 use serde::Serialize;
 use serde_json::json;
 use std::collections::{HashMap, HashSet};
 use std::fs;
 use std::fs::File;
-use std::io::Read;
 use std::io::Write;
-use std::io::{BufReader, BufWriter};
+use std::io::{BufRead, BufReader, BufWriter};
 use std::str::FromStr;
 use std::string::ToString;
 use std::sync::atomic::{AtomicUsize, Ordering};
@@ -39,7 +36,6 @@ use flate2::Compression;
 
 use crate::em::{em_optimize, em_optimize_subset, run_bootstrap, EmInitType};
 use crate::eq_class::{EqMap, EqMapType, IndexedEqList};
-use crate::io_utils;
 use crate::prog_opts::QuantOpts;
 use crate::pugutils;
 use crate::utils as afutils;
@@ -323,7 +319,7 @@ pub fn quantify(quant_opts: QuantOpts) -> anyhow::Result<()> {
     if compressed_input {
         let i_file =
             File::open(parent.join("map.collated.rad.sz")).context("run collate before quant")?;
-        let br = snap::read::FrameDecoder::new(BufReader::new(&i_file));
+        let br = BufReader::new(snap::read::FrameDecoder::new(BufReader::new(&i_file)));
 
         info!(
             log,
@@ -347,7 +343,7 @@ pub fn quantify(quant_opts: QuantOpts) -> anyhow::Result<()> {
 
 // TODO: see if we'd rather pass an structure
 // with these options
-pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<()> {
+pub fn do_quantify<T: BufRead>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<()> {
     let parent = std::path::Path::new(quant_opts.input_dir);
 
     let prelude = RadPrelude::from_bytes(&mut br)?;
@@ -486,8 +482,6 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
         .expect("tag map must contain cblen");
     let barcode_len: u16 = barcode_tag.try_into()?;
 
-    let record_context = prelude.get_record_context::<AlevinFryRecordContext>()?;
-
     // if we have a filter list, extract it here
     let mut retained_bc: Option<HashSet<u64, ahash::RandomState>> = None;
     if let Some(fname) = filter_list {
@@ -538,7 +532,10 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
     } else {
         1
     };
-    let q = Arc::new(ArrayQueue::<io_utils::MetaChunk>::new(4 * n_workers));
+    let mut chunk_reader = libradicl::readers::ParallelChunkReader::<AlevinFryReadRecord>::new(
+        &prelude,
+        std::num::NonZeroUsize::new(n_workers).unwrap(),
+    );
 
     // the number of cells left to process
     let cells_to_process = Arc::new(AtomicUsize::new(num_cells as usize));
@@ -644,7 +641,9 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
     // for each worker, spawn off a thread
     for _worker in 0..n_workers {
         // each thread will need to access the work queue
-        let in_q = q.clone();
+        //let in_q = q.clone();
+        let in_q = chunk_reader.get_queue();
+        let is_done = chunk_reader.is_done();
         // and the logger
         let log = log.clone();
         // the shared tid_to_gid map
@@ -652,12 +651,6 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
         // and the atomic counter of remaining work
         let cells_remaining = cells_to_process.clone();
 
-        let record_context = record_context.clone();
-        // TODO -- maybe delete March 5, 2024
-        // they will need to know the bc and umi type
-        // let bc_type = bc_type;
-        // let umi_type = umi_type;
-
         // and the file writer
         let bcout = bc_writer.clone();
         // global gene-level eqc map
@@ -735,32 +728,17 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
             let mut local_nrec = 0usize;
             // pop MetaChunks from the work queue until everything is
             // processed
-            while cells_remaining.load(Ordering::SeqCst) > 0 {
-                if let Some((
-                    first_cell_in_chunk,
-                    cells_in_chunk,
-                    _nbytes_total,
-                    _nrec_total,
-                    buf,
-                )) = in_q.pop()
-                {
-                    // for every cell (chunk) within this meta-chunk
-                    let mut byte_offset = 0usize;
-                    for cn in 0..cells_in_chunk {
+            while !is_done.load(Ordering::SeqCst) {
+                while let Some(meta_chunk) = in_q.pop() {
+                    let first_cell_in_chunk = meta_chunk.first_chunk_index;
+                    for (cn, mut c) in meta_chunk.iter().enumerate() {
                         cells_remaining.fetch_sub(1, Ordering::SeqCst);
                         let cell_num = first_cell_in_chunk + cn;
-                        // nbytes for the current cell
-                        let nbytes = buf[byte_offset..].pread::<u32>(0).unwrap();
-                        let nrec = buf[byte_offset..].pread::<u32>(4).unwrap();
+
+                        let nbytes = c.nbytes;
+                        let nrec = c.nrec;
                         local_nrec += nrec as usize;
-                        let mut nbr =
-                            BufReader::new(&buf[byte_offset..(byte_offset + nbytes as usize)]);
-                        byte_offset += nbytes as usize;
 
-                        let mut c = chunk::Chunk::<AlevinFryReadRecord>::from_bytes(
-                            &mut nbr,
-                            &record_context,
-                        );
                         if c.reads.is_empty() {
                             warn!(log, "Discovered empty chunk; should not happen! cell_num = {}, nbytes = {}, nrec = {}", cell_num, nbytes, nrec);
                         }
@@ -1214,22 +1192,22 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
         thread_handles.push(handle);
     }
 
+    let cb = |_new_bytes: u64, new_rec: u64| {
+        pbar.inc(new_rec);
+    };
+
     // push the work onto the queue for the worker threads
     // we spawned above.
-    if let Some(ret_bc) = retained_bc {
-        // we have a retained set
-        io_utils::fill_work_queue_filtered(
-            ret_bc,
-            &record_context,
-            q,
-            br,
-            hdr.num_chunks as usize,
-            &pbar,
-        )?;
+    let _ = if let Some(ret_bc) = retained_bc {
+        let filter_fn = |buf: &[u8], record_context: &AlevinFryRecordContext| -> bool {
+            let (bc, _umi) =
+                chunk::Chunk::<AlevinFryReadRecord>::peek_record(&buf[8..], record_context);
+            ret_bc.contains(&bc)
+        };
+        chunk_reader.start_filtered(&mut br, filter_fn, Some(cb))
     } else {
-        // we're quantifying everything
-        io_utils::fill_work_queue(q, br, hdr.num_chunks as usize, &pbar)?;
-    }
+        chunk_reader.start(&mut br, Some(cb))
+    };
 
     let gn_path = output_matrix_path.join("quants_mat_cols.txt");
     let gn_file = File::create(gn_path).expect("couldn't create gene name file.");