diff --git a/Cargo.lock b/Cargo.lock
index 26619e3..09b2060 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -10,21 +10,22 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
 
 [[package]]
 name = "ahash"
-version = "0.8.3"
+version = "0.8.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f"
+checksum = "e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011"
 dependencies = [
  "cfg-if",
  "getrandom",
  "once_cell",
  "version_check",
+ "zerocopy",
 ]
 
 [[package]]
 name = "aho-corasick"
-version = "1.0.2"
+version = "1.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "43f6cb1bf222025340178f382c426f13757b2960e89779dfcb319c32542a5a41"
+checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0"
 dependencies = [
  "memchr",
 ]
@@ -50,11 +51,12 @@ dependencies = [
  "libradicl",
  "mimalloc",
  "needletail",
+ "noodles",
+ "noodles-util",
  "num-format",
  "num_cpus",
  "petgraph",
  "rand",
- "rust-htslib",
  "sce",
  "scroll",
  "serde",
@@ -98,58 +100,57 @@ dependencies = [
 
 [[package]]
 name = "anstream"
-version = "0.3.2"
+version = "0.6.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163"
+checksum = "d96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb"
 dependencies = [
  "anstyle",
  "anstyle-parse",
  "anstyle-query",
  "anstyle-wincon",
  "colorchoice",
- "is-terminal",
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle"
-version = "1.0.1"
+version = "1.0.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3a30da5c5f2d5e72842e00bcb57657162cdabef0931f40e2deb9b4140440cecd"
+checksum = "8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.1"
+version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "938874ff5980b03a87c5524b3ae5b59cf99b1d6bc836848df7bc5ada9643c333"
+checksum = "c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.0.0"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b"
+checksum = "e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648"
 dependencies = [
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "1.0.1"
+version = "3.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188"
+checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7"
 dependencies = [
  "anstyle",
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "anyhow"
-version = "1.0.71"
+version = "1.0.80"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8"
+checksum = "5ad32ce52e4161730f7098c077cd2ed6229b5804ccf99e5366be1ab72a98b4e1"
 
 [[package]]
 name = "approx"
@@ -175,17 +176,6 @@ version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "96d30a06541fbafbc7f82ed10c06164cfbd2c401138f6addd8404629c4b16711"
 
-[[package]]
-name = "atty"
-version = "0.2.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
-dependencies = [
- "hermit-abi 0.1.19",
- "libc",
- "winapi",
-]
-
 [[package]]
 name = "autocfg"
 version = "1.1.0"
@@ -203,9 +193,9 @@ dependencies = [
 
 [[package]]
 name = "bio-types"
-version = "1.0.0"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c915bf6c578d40e1e497f8c571a4514bc89c3195cec2abb8be6dd5500405c752"
+checksum = "9d45749b87f21808051025e9bf714d14ff4627f9d8ca967eade6946ea769aa4a"
 dependencies = [
  "derive-new",
  "lazy_static",
@@ -215,57 +205,82 @@ dependencies = [
  "thiserror",
 ]
 
+[[package]]
+name = "bit-vec"
+version = "0.6.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
+
 [[package]]
 name = "bitflags"
 version = "1.3.2"
 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"
+
+[[package]]
+name = "block-buffer"
+version = "0.10.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71"
+dependencies = [
+ "generic-array",
+]
+
 [[package]]
 name = "bstr"
-version = "1.5.0"
+version = "1.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a246e68bb43f6cd9db24bea052a53e40405417c5fb372e3d1a8a7f770a564ef5"
+checksum = "05efc5cfd9110c8416e471df0e96702d58690178e206e61b7173706673c93706"
 dependencies = [
  "memchr",
- "once_cell",
  "regex-automata",
  "serde",
 ]
 
 [[package]]
 name = "buffer-redux"
-version = "1.0.0"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d2886ea01509598caac116942abd33ab5a88fa32acdf7e4abfa0fc489ca520c9"
+checksum = "4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5"
 dependencies = [
  "memchr",
- "safemem",
 ]
 
 [[package]]
 name = "bumpalo"
-version = "3.13.0"
+version = "3.15.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a3e2c3daef883ecc1b5d58c15adae93470a91d425f3532ba1695849656af3fc1"
+checksum = "7ff69b9dd49fd426c69a0db9fc04dd934cdb6645ff000864d98f7e2af8830eaa"
 
 [[package]]
 name = "bytecount"
-version = "0.6.3"
+version = "0.6.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2c676a478f63e9fa2dd5368a42f28bba0d6c560b775f38583c8bbaa7fcd67c9c"
+checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205"
 
 [[package]]
 name = "bytemuck"
-version = "1.13.1"
+version = "1.14.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "17febce684fd15d89027105661fec94afb475cb995fbc59d2865198446ba2eea"
+checksum = "a2ef034f05691a48569bd920a96c81b9d91bbad1ab5ac7c4616c1f6ef36cb79f"
 
 [[package]]
 name = "byteorder"
-version = "1.4.3"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610"
+checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
+
+[[package]]
+name = "bytes"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223"
 
 [[package]]
 name = "bzip2"
@@ -290,12 +305,9 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.0.79"
+version = "1.0.90"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f"
-dependencies = [
- "jobserver",
-]
+checksum = "8cd6604a82acf3039f1144f54b8eb34e91ffba622051189e71b781822d5ee1f5"
 
 [[package]]
 name = "cfg-if"
@@ -305,71 +317,58 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
 [[package]]
 name = "chrono"
-version = "0.4.26"
+version = "0.4.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ec837a71355b28f6556dbd569b37b3f363091c0bd4b2e735674521b4c5fd9bc5"
+checksum = "8eaf5903dcbc0a39312feb77df2ff4c76387d591b9fc7b04a238dcf8bb62639a"
 dependencies = [
  "android-tzdata",
  "iana-time-zone",
  "js-sys",
  "num-traits",
- "time 0.1.45",
  "wasm-bindgen",
- "winapi",
+ "windows-targets 0.52.4",
 ]
 
 [[package]]
 name = "clap"
-version = "4.3.9"
+version = "4.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bba77a07e4489fb41bd90e8d4201c3eb246b3c2c9ea2ba0bddd6c1d1df87db7d"
+checksum = "b230ab84b0ffdf890d5a10abdbc8b83ae1c4918275daea1ab8801f71536b2651"
 dependencies = [
  "clap_builder",
  "clap_derive",
- "once_cell",
 ]
 
 [[package]]
 name = "clap_builder"
-version = "4.3.9"
+version = "4.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2c9b4a88bb4bc35d3d6f65a21b0f0bafe9c894fa00978de242c555ec28bea1c0"
+checksum = "ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4"
 dependencies = [
  "anstream",
  "anstyle",
- "bitflags",
  "clap_lex",
- "once_cell",
  "strsim",
  "terminal_size",
 ]
 
 [[package]]
 name = "clap_derive"
-version = "4.3.2"
+version = "4.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b8cd2b2a819ad6eec39e8f1d6b53001af1e5469f8c177579cdaeb313115b825f"
+checksum = "307bc0538d5f0f83b8248db3087aa92fe504e4691294d0c96c0eabc33f47ba47"
 dependencies = [
  "heck",
  "proc-macro2",
  "quote",
- "syn 2.0.22",
+ "syn 2.0.52",
 ]
 
 [[package]]
 name = "clap_lex"
-version = "0.5.0"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2da6da31387c7e4ef160ffab6d5e7f00c42626fe39aea70a7b0f1773f7dd6c1b"
-
-[[package]]
-name = "cmake"
-version = "0.1.50"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130"
-dependencies = [
- "cc",
-]
+checksum = "98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce"
 
 [[package]]
 name = "colorchoice"
@@ -379,90 +378,90 @@ checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7"
 
 [[package]]
 name = "console"
-version = "0.15.7"
+version = "0.15.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c926e00cc70edefdc64d3a5ff31cc65bb97a3460097762bd23afb4d8145fccf8"
+checksum = "0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb"
 dependencies = [
  "encode_unicode",
  "lazy_static",
  "libc",
  "unicode-width",
- "windows-sys 0.45.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "core-foundation-sys"
-version = "0.8.4"
+version = "0.8.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e496a50fda8aacccc86d7529e2c1e0892dbd0f898a6b5645b5561b89c3210efa"
+checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f"
 
 [[package]]
 name = "crc32fast"
-version = "1.3.2"
+version = "1.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d"
+checksum = "b3855a8a784b474f333699ef2bbca9db2c4a1f6d9088a90a2d25b1eb53111eaa"
 dependencies = [
  "cfg-if",
 ]
 
 [[package]]
 name = "crossbeam-channel"
-version = "0.5.8"
+version = "0.5.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a33c2bf77f2df06183c3aa30d1e96c0695a313d4f9c453cc3762a6db39f99200"
+checksum = "ab3db02a9c5b5121e1e42fbdb1aeb65f5e02624cc58c43f2884c6ccac0b82f95"
 dependencies = [
- "cfg-if",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-deque"
-version = "0.8.3"
+version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef"
+checksum = "613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d"
 dependencies = [
- "cfg-if",
  "crossbeam-epoch",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-epoch"
-version = "0.9.15"
+version = "0.9.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7"
+checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e"
 dependencies = [
- "autocfg",
- "cfg-if",
  "crossbeam-utils",
- "memoffset",
- "scopeguard",
 ]
 
 [[package]]
 name = "crossbeam-queue"
-version = "0.3.8"
+version = "0.3.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d1cfb3ea8a53f37c40dea2c7bedcbd88bdfae54f5e2175d6ecaff1c988353add"
+checksum = "df0346b5d5e76ac2fe4e327c5fd1118d6be7c51dfb18f9b7922923f287471e35"
 dependencies = [
- "cfg-if",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-utils"
-version = "0.8.16"
+version = "0.8.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294"
+checksum = "248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345"
+
+[[package]]
+name = "crypto-common"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3"
 dependencies = [
- "cfg-if",
+ "generic-array",
+ "typenum",
 ]
 
 [[package]]
 name = "csv"
-version = "1.2.2"
+version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "626ae34994d3d8d668f4269922248239db4ae42d538b14c398b74a52208e8086"
+checksum = "ac574ff4d437a7b5ad237ef331c17ccca63c46479e5b5453eb8e10bb99a759fe"
 dependencies = [
  "csv-core",
  "itoa",
@@ -472,24 +471,18 @@ dependencies = [
 
 [[package]]
 name = "csv-core"
-version = "0.1.10"
+version = "0.1.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90"
+checksum = "5efa2b3d7902f4b634a20cae3c9c4e6209dc4779feb6863329607560143efa70"
 dependencies = [
  "memchr",
 ]
 
-[[package]]
-name = "custom_derive"
-version = "0.1.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
-
 [[package]]
 name = "dashmap"
-version = "5.4.0"
+version = "5.5.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "907076dfda823b0b36d2a1bb5f90c96660a5bbcd7729e10727f07858f22c4edc"
+checksum = "978747c1d849a7d2ee5e8adc0159961c48fb7e5db2f06af6723b80123bb53856"
 dependencies = [
  "cfg-if",
  "hashbrown",
@@ -498,6 +491,15 @@ dependencies = [
  "parking_lot_core",
 ]
 
+[[package]]
+name = "deranged"
+version = "0.3.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4"
+dependencies = [
+ "powerfmt",
+]
+
 [[package]]
 name = "derive-new"
 version = "0.5.9"
@@ -509,6 +511,16 @@ dependencies = [
  "syn 1.0.109",
 ]
 
+[[package]]
+name = "digest"
+version = "0.10.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292"
+dependencies = [
+ "block-buffer",
+ "crypto-common",
+]
+
 [[package]]
 name = "dirs-next"
 version = "2.0.0"
@@ -532,9 +544,9 @@ dependencies = [
 
 [[package]]
 name = "either"
-version = "1.8.1"
+version = "1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7fcaabb2fef8c910e7f4c7ce9f67a1283a1715879a7c230ca9d6d1ae31f16d91"
+checksum = "11157ac094ffbdde99aa67b23417ebdd801842852b500e395a45a9c0aac03e4a"
 
 [[package]]
 name = "encode_unicode"
@@ -543,24 +555,19 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f"
 
 [[package]]
-name = "errno"
-version = "0.3.1"
+name = "equivalent"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4bcfec3a70f97c962c307b2d2c56e358cf1d00b558d74262b5f929ee8cc7e73a"
-dependencies = [
- "errno-dragonfly",
- "libc",
- "windows-sys 0.48.0",
-]
+checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
 
 [[package]]
-name = "errno-dragonfly"
-version = "0.1.2"
+name = "errno"
+version = "0.3.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf"
+checksum = "a258e46cdc063eb8519c00b9fc845fc47bcfca4130e2f08e88665ceda8474245"
 dependencies = [
- "cc",
  "libc",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -571,54 +578,40 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
 [[package]]
 name = "flate2"
-version = "1.0.26"
+version = "1.0.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3b9429470923de8e8cbd4d2dc513535400b4b3fef0319fb5c4e1f520a7bef743"
+checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e"
 dependencies = [
  "crc32fast",
  "miniz_oxide",
 ]
 
 [[package]]
-name = "form_urlencoded"
-version = "1.2.0"
+name = "generic-array"
+version = "0.14.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652"
+checksum = "85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a"
 dependencies = [
- "percent-encoding",
-]
-
-[[package]]
-name = "fs-utils"
-version = "1.1.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6fc7a9dc005c944c98a935e7fd626faf5bf7e5a609f94bc13e42fc4a02e52593"
-dependencies = [
- "quick-error",
+ "typenum",
+ "version_check",
 ]
 
 [[package]]
 name = "getrandom"
-version = "0.2.10"
+version = "0.2.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427"
+checksum = "190092ea657667030ac6a35e305e62fc4dd69fd98ac98631e5d3a2b1575a12b5"
 dependencies = [
  "cfg-if",
  "libc",
- "wasi 0.11.0+wasi-snapshot-preview1",
+ "wasi",
 ]
 
-[[package]]
-name = "glob"
-version = "0.3.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
-
 [[package]]
 name = "hashbrown"
-version = "0.12.3"
+version = "0.14.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888"
+checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604"
 
 [[package]]
 name = "heck"
@@ -628,45 +621,22 @@ checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
 [[package]]
 name = "hermit-abi"
-version = "0.1.19"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33"
-dependencies = [
- "libc",
-]
-
-[[package]]
-name = "hermit-abi"
-version = "0.3.1"
+version = "0.3.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fed44880c466736ef9a5c5b5facefb5ed0785676d0c02d612db14e54f0d84286"
-
-[[package]]
-name = "hts-sys"
-version = "2.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "deebfb779c734d542e7f14c298597914b9b5425e4089aef482eacb5cab941915"
-dependencies = [
- "bzip2-sys",
- "cc",
- "fs-utils",
- "glob",
- "libz-sys",
- "lzma-sys",
-]
+checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024"
 
 [[package]]
 name = "iana-time-zone"
-version = "0.1.57"
+version = "0.1.60"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2fad5b825842d2b38bd206f3e81d6957625fd7f0a361e345c30e01a0ae2dd613"
+checksum = "e7ffbb5a1b541ea2561f8c41c087286cc091e21e556a4f09a8f6cbf17b69b141"
 dependencies = [
  "android_system_properties",
  "core-foundation-sys",
  "iana-time-zone-haiku",
  "js-sys",
  "wasm-bindgen",
- "windows",
+ "windows-core",
 ]
 
 [[package]]
@@ -678,37 +648,21 @@ dependencies = [
  "cc",
 ]
 
-[[package]]
-name = "idna"
-version = "0.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7d20d6b07bfbc108882d88ed8e37d39636dcc260e15e30c45e6ba089610b917c"
-dependencies = [
- "unicode-bidi",
- "unicode-normalization",
-]
-
-[[package]]
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-version = "0.2.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c"
-
 [[package]]
 name = "indexmap"
-version = "1.9.3"
+version = "2.2.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99"
+checksum = "7b0b929d511467233429c45a44ac1dcaa21ba0f5ba11e4879e6ed28ddb4f9df4"
 dependencies = [
- "autocfg",
+ "equivalent",
  "hashbrown",
 ]
 
 [[package]]
 name = "indicatif"
-version = "0.17.5"
+version = "0.17.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8ff8cc23a7393a397ed1d7f56e6365cba772aba9f9912ab968b03043c395d057"
+checksum = "763a5a8f45087d6bcea4222e7b72c291a054edf80e4ef6efd2a4979878c7bea3"
 dependencies = [
  "console",
  "instant",
@@ -727,84 +681,127 @@ dependencies = [
 ]
 
 [[package]]
-name = "io-lifetimes"
-version = "1.0.11"
+name = "is-terminal"
+version = "0.4.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "eae7b9aee968036d54dce06cebaefd919e4472e753296daccd6d344e3e2df0c2"
+checksum = "f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b"
 dependencies = [
- "hermit-abi 0.3.1",
+ "hermit-abi",
  "libc",
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
-name = "is-terminal"
-version = "0.4.7"
+name = "itertools"
+version = "0.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adcf93614601c8129ddf72e2d5633df827ba6551541c6d8c59520a371475be1f"
+checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569"
 dependencies = [
- "hermit-abi 0.3.1",
- "io-lifetimes",
- "rustix",
- "windows-sys 0.48.0",
+ "either",
 ]
 
 [[package]]
-name = "itertools"
-version = "0.11.0"
+name = "itoa"
+version = "1.0.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57"
+checksum = "b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c"
+
+[[package]]
+name = "js-sys"
+version = "0.3.69"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d"
 dependencies = [
- "either",
+ "wasm-bindgen",
 ]
 
 [[package]]
-name = "itoa"
-version = "1.0.6"
+name = "lazy_static"
+version = "1.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "453ad9f582a441959e5f0d088b02ce04cfe8d51a8eaf077f12ac6d3e94164ca6"
+checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
 
 [[package]]
-name = "jobserver"
-version = "0.1.26"
+name = "lexical-core"
+version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "936cfd212a0155903bcbc060e316fb6cc7cbf2e1907329391ebadc1fe0ce77c2"
+checksum = "2cde5de06e8d4c2faabc400238f9ae1c74d5412d03a7bd067645ccbc47070e46"
 dependencies = [
- "libc",
+ "lexical-parse-float",
+ "lexical-parse-integer",
+ "lexical-util",
+ "lexical-write-float",
+ "lexical-write-integer",
 ]
 
 [[package]]
-name = "js-sys"
-version = "0.3.64"
+name = "lexical-parse-float"
+version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c5f195fe497f702db0f318b07fdd68edb16955aed830df8363d837542f8f935a"
+checksum = "683b3a5ebd0130b8fb52ba0bdc718cc56815b6a097e28ae5a6997d0ad17dc05f"
 dependencies = [
- "wasm-bindgen",
+ "lexical-parse-integer",
+ "lexical-util",
+ "static_assertions",
 ]
 
 [[package]]
-name = "lazy_static"
-version = "1.4.0"
+name = "lexical-parse-integer"
+version = "0.8.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+checksum = "6d0994485ed0c312f6d965766754ea177d07f9c00c9b82a5ee62ed5b47945ee9"
+dependencies = [
+ "lexical-util",
+ "static_assertions",
+]
+
+[[package]]
+name = "lexical-util"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5255b9ff16ff898710eb9eb63cb39248ea8a5bb036bea8085b1a767ff6c4e3fc"
+dependencies = [
+ "static_assertions",
+]
+
+[[package]]
+name = "lexical-write-float"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "accabaa1c4581f05a3923d1b4cfd124c329352288b7b9da09e766b0668116862"
+dependencies = [
+ "lexical-util",
+ "lexical-write-integer",
+ "static_assertions",
+]
+
+[[package]]
+name = "lexical-write-integer"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e1b6f3d1f4422866b68192d62f77bc5c700bee84f3069f2469d7bc8c77852446"
+dependencies = [
+ "lexical-util",
+ "static_assertions",
+]
 
 [[package]]
 name = "libc"
-version = "0.2.147"
+version = "0.2.153"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b4668fb0ea861c1df094127ac5f1da3409a82116a4ba74fca2e58ef927159bb3"
+checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
 
 [[package]]
 name = "libm"
-version = "0.2.7"
+version = "0.2.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f7012b1bbb0719e1097c47611d3898568c546d597c2e74d66f6087edd5233ff4"
+checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
 [[package]]
 name = "libmimalloc-sys"
-version = "0.1.33"
+version = "0.1.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f4ac0e912c8ef1b735e92369695618dc5b1819f5a7bf3f167301a3ba1cea515e"
+checksum = "3979b5c37ece694f1f5e51e7ecc871fdb0f517ed04ee45f88d15d6d553cb9664"
 dependencies = [
  "cc",
  "libc",
@@ -812,14 +809,16 @@ dependencies = [
 
 [[package]]
 name = "libradicl"
-version = "0.6.0"
-source = "git+https://github.com/COMBINE-lab/libradicl?branch=develop#ea255cc40219192feb328d75e485886341853f0b"
+version = "0.8.2"
+source = "git+https://github.com/COMBINE-lab/libradicl?branch=develop#d10845e2a96f4eaf0a14f8aee136bdc0c8330acb"
 dependencies = [
  "ahash",
+ "anyhow",
  "bio-types",
  "dashmap",
+ "noodles-bam",
+ "noodles-sam",
  "num",
- "rust-htslib",
  "scroll",
  "serde",
  "smallvec",
@@ -827,35 +826,27 @@ dependencies = [
 ]
 
 [[package]]
-name = "libz-sys"
-version = "1.1.9"
+name = "libredox"
+version = "0.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "56ee889ecc9568871456d42f603d6a0ce59ff328d291063a45cbdf0036baf6db"
+checksum = "85c833ca1e66078851dba29046874e38f08b2c883700aa29a03ddd3b23814ee8"
 dependencies = [
- "cc",
- "cmake",
+ "bitflags 2.4.2",
  "libc",
- "pkg-config",
- "vcpkg",
+ "redox_syscall",
 ]
 
-[[package]]
-name = "linear-map"
-version = "1.2.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
-
 [[package]]
 name = "linux-raw-sys"
-version = "0.3.8"
+version = "0.4.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef53942eb7bf7ff43a617b3e2c1c4a5ecf5944a7c1bc12d7ee39bbb15e5c1519"
+checksum = "01cda141df6706de531b6c46c3a33ecca755538219bd484262fa09410c13539c"
 
 [[package]]
 name = "lock_api"
-version = "0.4.10"
+version = "0.4.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16"
+checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
 dependencies = [
  "autocfg",
  "scopeguard",
@@ -863,9 +854,9 @@ dependencies = [
 
 [[package]]
 name = "log"
-version = "0.4.19"
+version = "0.4.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b06a4cde4c0f271a446782e3eff8de789548ce57dbc8eca9292c27f4a42004b4"
+checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
 
 [[package]]
 name = "lzma-sys"
@@ -880,43 +871,44 @@ dependencies = [
 
 [[package]]
 name = "matrixmultiply"
-version = "0.3.7"
+version = "0.3.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "090126dc04f95dc0d1c1c91f61bdd474b3930ca064c1edc8a849da2c6cbe1e77"
+checksum = "7574c1cf36da4798ab73da5b215bbf444f50718207754cb522201d78d1cd0ff2"
 dependencies = [
  "autocfg",
  "rawpointer",
 ]
 
 [[package]]
-name = "memchr"
-version = "2.5.0"
+name = "md-5"
+version = "0.10.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d"
+checksum = "d89e7ee0cfbedfc4da3340218492196241d89eefb6dab27de5df917a6d2e78cf"
+dependencies = [
+ "cfg-if",
+ "digest",
+]
 
 [[package]]
-name = "memoffset"
-version = "0.9.0"
+name = "memchr"
+version = "2.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c"
-dependencies = [
- "autocfg",
-]
+checksum = "523dc4f511e55ab87b694dc30d0f820d60906ef06413f93d4d7a1385599cc149"
 
 [[package]]
 name = "mimalloc"
-version = "0.1.37"
+version = "0.1.39"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4e2894987a3459f3ffb755608bd82188f8ed00d0ae077f1edea29c068d639d98"
+checksum = "fa01922b5ea280a911e323e4d2fd24b7fe5cc4042e0d2cda3c40775cdc4bdc9c"
 dependencies = [
  "libmimalloc-sys",
 ]
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.1"
+version = "0.7.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7"
+checksum = "9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7"
 dependencies = [
  "adler",
 ]
@@ -930,7 +922,7 @@ dependencies = [
  "approx 0.5.1",
  "matrixmultiply",
  "nalgebra-macros",
- "num-complex 0.4.3",
+ "num-complex 0.4.5",
  "num-rational",
  "num-traits",
  "rand",
@@ -957,7 +949,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32"
 dependencies = [
  "matrixmultiply",
- "num-complex 0.4.3",
+ "num-complex 0.4.5",
  "num-integer",
  "num-traits",
  "rawpointer",
@@ -978,22 +970,137 @@ dependencies = [
 ]
 
 [[package]]
-name = "newtype_derive"
-version = "0.1.6"
+name = "noodles"
+version = "0.65.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "38db1833ba39368f7a855c5b9a8412729a61dd86b2563e1a3bdb02aecbe92a3c"
+dependencies = [
+ "noodles-bam",
+ "noodles-bgzf",
+ "noodles-sam",
+]
+
+[[package]]
+name = "noodles-bam"
+version = "0.56.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d3189e8ecee801ab5c3f4ea9908c4196b429137d8d35d733f00f6681f9188be7"
+dependencies = [
+ "bit-vec",
+ "bstr",
+ "byteorder",
+ "bytes",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
+ "noodles-sam",
+]
+
+[[package]]
+name = "noodles-bgzf"
+version = "0.26.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8970db2e84adb1007377dd3988258d7a64e3fc4c05602ebf94e1f8cba207c030"
+dependencies = [
+ "byteorder",
+ "bytes",
+ "crossbeam-channel",
+ "flate2",
+]
+
+[[package]]
+name = "noodles-core"
+version = "0.14.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7336c3be652de4e05444c9b12a32331beb5ba3316e8872d92bfdd8ef3b06c282"
+
+[[package]]
+name = "noodles-cram"
+version = "0.56.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec"
+checksum = "34a70ebb5bc7ff2d07ce96c0568691e57be421c121103ebef10cf02a63d7d400"
 dependencies = [
- "rustc_version",
+ "bitflags 2.4.2",
+ "bstr",
+ "byteorder",
+ "bytes",
+ "bzip2",
+ "flate2",
+ "indexmap",
+ "md-5",
+ "noodles-bam",
+ "noodles-core",
+ "noodles-fasta",
+ "noodles-sam",
+ "xz2",
+]
+
+[[package]]
+name = "noodles-csi"
+version = "0.30.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a60dfe0919f7ecbd081a82eb1d32e8f89f9041932d035fe8309073c8c01277bf"
+dependencies = [
+ "bit-vec",
+ "byteorder",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core",
+]
+
+[[package]]
+name = "noodles-fasta"
+version = "0.33.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5e9e953e4e90e6c96e6a384598ebf2ab6d2f5add259ff05a194cf635e892c980"
+dependencies = [
+ "bytes",
+ "memchr",
+ "noodles-bgzf",
+ "noodles-core",
+]
+
+[[package]]
+name = "noodles-sam"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1f0d8e441368374f6e144989f823fd7c05e58cdaa3f97d22bb4d75b534327b87"
+dependencies = [
+ "bitflags 2.4.2",
+ "bstr",
+ "indexmap",
+ "lexical-core",
+ "memchr",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
+]
+
+[[package]]
+name = "noodles-util"
+version = "0.37.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e800d2619f75de004aef8beb29f604e667f5bf5f714ff05cce3730f5c8cc4958"
+dependencies = [
+ "flate2",
+ "noodles-bam",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-cram",
+ "noodles-csi",
+ "noodles-fasta",
+ "noodles-sam",
 ]
 
 [[package]]
 name = "num"
-version = "0.4.0"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "43db66d1170d347f9a065114077f7dccb00c1b9478c89384490a3425279a4606"
+checksum = "b05180d69e3da0e530ba2a1dae5110317e49e3b7f3d41be227dc5f92e49ee7af"
 dependencies = [
  "num-bigint",
- "num-complex 0.4.3",
+ "num-complex 0.4.5",
  "num-integer",
  "num-iter",
  "num-rational",
@@ -1002,9 +1109,9 @@ dependencies = [
 
 [[package]]
 name = "num-bigint"
-version = "0.4.3"
+version = "0.4.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f93ab6289c7b344a8a9f60f88d80aa20032336fe78da341afc91c8a2341fc75f"
+checksum = "608e7659b5c3d7cba262d894801b9ec9d00de989e8a82bd4bef91d08da45cdc0"
 dependencies = [
  "autocfg",
  "num-integer",
@@ -1023,13 +1130,19 @@ dependencies = [
 
 [[package]]
 name = "num-complex"
-version = "0.4.3"
+version = "0.4.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02e0d21255c828d6f128a1e41534206671e8c3ea0c62f32291e808dc82cff17d"
+checksum = "23c6602fda94a57c990fe0df199a035d83576b496aa29f4e634a8ac6004e68a6"
 dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "num-conv"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9"
+
 [[package]]
 name = "num-format"
 version = "0.4.4"
@@ -1042,19 +1155,18 @@ dependencies = [
 
 [[package]]
 name = "num-integer"
-version = "0.1.45"
+version = "0.1.46"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9"
+checksum = "7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f"
 dependencies = [
- "autocfg",
  "num-traits",
 ]
 
 [[package]]
 name = "num-iter"
-version = "0.1.43"
+version = "0.1.44"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7d03e6c028c5dc5cac6e2dec0efda81fc887605bb3d884578bb6d6bf7514e252"
+checksum = "d869c01cc0c455284163fd0092f1f93835385ccab5a98a0dcc497b2f8bf055a9"
 dependencies = [
  "autocfg",
  "num-integer",
@@ -1075,9 +1187,9 @@ dependencies = [
 
 [[package]]
 name = "num-traits"
-version = "0.2.15"
+version = "0.2.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd"
+checksum = "da0df0e5185db44f69b44f26786fe401b6c293d1907744beaa7fa62b2e5a517a"
 dependencies = [
  "autocfg",
  "libm",
@@ -1089,16 +1201,7 @@ version = "1.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43"
 dependencies = [
- "hermit-abi 0.3.1",
- "libc",
-]
-
-[[package]]
-name = "num_threads"
-version = "0.1.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2819ce041d2ee131036f4fc9d6ae7ae125a3a40e97ba64d04fe799ad9dabbb44"
-dependencies = [
+ "hermit-abi",
  "libc",
 ]
 
@@ -1110,40 +1213,34 @@ checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
 
 [[package]]
 name = "once_cell"
-version = "1.18.0"
+version = "1.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d"
+checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
 
 [[package]]
 name = "parking_lot_core"
-version = "0.9.8"
+version = "0.9.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "93f00c865fe7cabf650081affecd3871070f26767e7b2070a3ffae14c654b447"
+checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e"
 dependencies = [
  "cfg-if",
  "libc",
- "redox_syscall 0.3.5",
+ "redox_syscall",
  "smallvec",
- "windows-targets 0.48.1",
+ "windows-targets 0.48.5",
 ]
 
 [[package]]
 name = "paste"
-version = "1.0.12"
+version = "1.0.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9f746c4065a8fa3fe23974dd82f15431cc8d40779821001404d10d2e79ca7d79"
-
-[[package]]
-name = "percent-encoding"
-version = "2.3.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9b2a4787296e9989611394c33f193f676704af1686e70b8f8033ab5ba9a35a94"
+checksum = "de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c"
 
 [[package]]
 name = "petgraph"
-version = "0.6.3"
+version = "0.6.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4dd7d28ee937e54fe3080c91faa1c3a46c06de6252988a7f4592ba2310ef22a4"
+checksum = "e1d3afd2628e69da2be385eb6f2fd57c8ac7977ceeff6dc166ff1657b0e386a9"
 dependencies = [
  "fixedbitset",
  "indexmap",
@@ -1151,15 +1248,21 @@ dependencies = [
 
 [[package]]
 name = "pkg-config"
-version = "0.3.27"
+version = "0.3.30"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964"
+checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec"
 
 [[package]]
 name = "portable-atomic"
-version = "1.3.3"
+version = "1.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "767eb9f07d4a5ebcb39bbf2d452058a93c011373abf6832e24194a1c3f004794"
+checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0"
+
+[[package]]
+name = "powerfmt"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391"
 
 [[package]]
 name = "ppv-lite86"
@@ -1169,24 +1272,18 @@ checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.63"
+version = "1.0.78"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b368fba921b0dce7e60f5e04ec15e565b3303972b42bcfde1d0713b881959eb"
+checksum = "e2422ad645d89c99f8f3e6b88a9fdeca7fabeac836b1002371c4367c8f984aae"
 dependencies = [
  "unicode-ident",
 ]
 
-[[package]]
-name = "quick-error"
-version = "1.2.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
-
 [[package]]
 name = "quote"
-version = "1.0.29"
+version = "1.0.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "573015e8ab27661678357f27dc26460738fd2b6c86e46f386fde94cb5d913105"
+checksum = "291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef"
 dependencies = [
  "proc-macro2",
 ]
@@ -1239,9 +1336,9 @@ checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
 
 [[package]]
 name = "rayon"
-version = "1.7.0"
+version = "1.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1d2df5196e37bcc87abebc0053e20787d73847bb33134a69841207dd0a47f03b"
+checksum = "e4963ed1bc86e4f3ee217022bd855b297cef07fb9eac5dfa1f788b220b49b3bd"
 dependencies = [
  "either",
  "rayon-core",
@@ -1249,139 +1346,97 @@ dependencies = [
 
 [[package]]
 name = "rayon-core"
-version = "1.11.0"
+version = "1.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4b8f95bd6966f5c87776639160a66bd8ab9895d9d4ab01ddba9fc60661aebe8d"
+checksum = "1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2"
 dependencies = [
- "crossbeam-channel",
  "crossbeam-deque",
  "crossbeam-utils",
- "num_cpus",
-]
-
-[[package]]
-name = "redox_syscall"
-version = "0.2.16"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a"
-dependencies = [
- "bitflags",
 ]
 
 [[package]]
 name = "redox_syscall"
-version = "0.3.5"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29"
+checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
 dependencies = [
- "bitflags",
+ "bitflags 1.3.2",
 ]
 
 [[package]]
 name = "redox_users"
-version = "0.4.3"
+version = "0.4.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b033d837a7cf162d7993aded9304e30a83213c648b6e389db233191f891e5c2b"
+checksum = "a18479200779601e498ada4e8c1e1f50e3ee19deb0259c25825a98b5603b2cb4"
 dependencies = [
  "getrandom",
- "redox_syscall 0.2.16",
+ "libredox",
  "thiserror",
 ]
 
 [[package]]
 name = "regex"
-version = "1.8.4"
+version = "1.10.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d0ab3ca65655bb1e41f2a8c8cd662eb4fb035e67c3f78da1d61dffe89d07300f"
+checksum = "b62dbe01f0b06f9d8dc7d49e05a0785f153b00b2c227856282f671e0318c9b15"
 dependencies = [
  "aho-corasick",
  "memchr",
+ "regex-automata",
  "regex-syntax",
 ]
 
 [[package]]
 name = "regex-automata"
-version = "0.1.10"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132"
-
-[[package]]
-name = "regex-syntax"
-version = "0.7.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "436b050e76ed2903236f032a59761c1eb99e1b0aead2c257922771dab1fc8c78"
-
-[[package]]
-name = "rust-htslib"
-version = "0.44.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7c7eb0f29fce64a4e22578905efef3d72389058016023279a58b282eb5c0c467"
+checksum = "86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea"
 dependencies = [
- "bio-types",
- "byteorder",
- "custom_derive",
- "derive-new",
- "hts-sys",
- "ieee754",
- "lazy_static",
- "libc",
- "linear-map",
- "newtype_derive",
- "regex",
- "thiserror",
- "url",
+ "aho-corasick",
+ "memchr",
+ "regex-syntax",
 ]
 
 [[package]]
-name = "rustc_version"
-version = "0.1.7"
+name = "regex-syntax"
+version = "0.8.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084"
-dependencies = [
- "semver",
-]
+checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f"
 
 [[package]]
 name = "rustix"
-version = "0.37.20"
+version = "0.38.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b96e891d04aa506a6d1f318d2771bcb1c7dfda84e126660ace067c9b474bb2c0"
+checksum = "6ea3e1a662af26cd7a3ba09c0297a31af215563ecf42817c98df621387f4e949"
 dependencies = [
- "bitflags",
+ "bitflags 2.4.2",
  "errno",
- "io-lifetimes",
  "libc",
  "linux-raw-sys",
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "rustversion"
-version = "1.0.12"
+version = "1.0.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4f3208ce4d8448b3f3e7d168a73f5e0c43a61e32930de3bceeccedb388b6bf06"
+checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4"
 
 [[package]]
 name = "ryu"
-version = "1.0.13"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f91339c0467de62360649f8d3e185ca8de4224ff281f66000de5eb2a77a79041"
+checksum = "e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1"
 
 [[package]]
 name = "safe_arch"
-version = "0.7.0"
+version = "0.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62a7484307bd40f8f7ccbacccac730108f2cae119a3b11c74485b48aa9ea650f"
+checksum = "f398075ce1e6a179b46f51bd88d0598b92b00d3551f1a2d4ac49e771b56ac354"
 dependencies = [
  "bytemuck",
 ]
 
-[[package]]
-name = "safemem"
-version = "0.3.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef703b7cb59335eae2eb93ceb664c0eb7ea6bf567079d843e09420219668e072"
-
 [[package]]
 name = "sce"
 version = "0.2.0"
@@ -1398,47 +1453,41 @@ dependencies = [
 
 [[package]]
 name = "scopeguard"
-version = "1.1.0"
+version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd"
+checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
 
 [[package]]
 name = "scroll"
-version = "0.11.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "04c565b551bafbef4157586fa379538366e4385d42082f255bfd96e4fe8519da"
-
-[[package]]
-name = "semver"
-version = "0.1.20"
+version = "0.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
+checksum = "6ab8598aa408498679922eff7fa985c25d58a90771bd6be794434c5277eab1a6"
 
 [[package]]
 name = "serde"
-version = "1.0.164"
+version = "1.0.197"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9e8c8cf938e98f769bc164923b06dce91cea1751522f46f8466461af04c9027d"
+checksum = "3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.164"
+version = "1.0.197"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d9735b638ccc51c28bf6914d90a2e9725b377144fc612c49a611fddd1b631d68"
+checksum = "7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.22",
+ "syn 2.0.52",
 ]
 
 [[package]]
 name = "serde_json"
-version = "1.0.99"
+version = "1.0.114"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46266871c240a00b8f503b877622fe33430b3c7d963bdc0f2adc511e54a1eae3"
+checksum = "c5f09b1bd632ef549eaa9f60a1f8de742bdbc698e6cee2095fc84dde5f549ae0"
 dependencies = [
  "itoa",
  "ryu",
@@ -1452,7 +1501,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f0b7840f121a46d63066ee7a99fc81dcabbc6105e437cae43528cea199b5a05f"
 dependencies = [
  "approx 0.5.1",
- "num-complex 0.4.3",
+ "num-complex 0.4.5",
  "num-traits",
  "paste",
  "wide",
@@ -1466,9 +1515,9 @@ checksum = "8347046d4ebd943127157b94d63abb990fcf729dc4e9978927fdf4ac3c998d06"
 
 [[package]]
 name = "slog-async"
-version = "2.7.0"
+version = "2.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "766c59b252e62a34651412870ff55d8c4e6d04df19b43eecb2703e417b097ffe"
+checksum = "72c8038f898a2c79507940990f05386455b3a317d8f18d4caea7cbc3d5096b84"
 dependencies = [
  "crossbeam-channel",
  "slog",
@@ -1478,28 +1527,28 @@ dependencies = [
 
 [[package]]
 name = "slog-term"
-version = "2.9.0"
+version = "2.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87d29185c55b7b258b4f120eab00f48557d4d9bc814f41713f449d35b0f8977c"
+checksum = "b6e022d0b998abfe5c3782c1f03551a596269450ccd677ea51c56f8b214610e8"
 dependencies = [
- "atty",
+ "is-terminal",
  "slog",
  "term",
  "thread_local",
- "time 0.3.22",
+ "time",
 ]
 
 [[package]]
 name = "smallvec"
-version = "1.10.0"
+version = "1.13.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0"
+checksum = "e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7"
 
 [[package]]
 name = "snap"
-version = "1.1.0"
+version = "1.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5e9f0ab6ef7eb7353d9119c170a436d1bf248eea575ac42d19d12f4e34130831"
+checksum = "1b6b67fb9a61334225b5b790716f609cd58395f895b3fe8b328786812a40bc3b"
 
 [[package]]
 name = "sprs"
@@ -1509,13 +1558,19 @@ checksum = "88bab60b0a18fb9b3e0c26e92796b3c3a278bf5fa4880f5ad5cc3bdfb843d0b1"
 dependencies = [
  "alga",
  "ndarray",
- "num-complex 0.4.3",
+ "num-complex 0.4.5",
  "num-traits",
  "num_cpus",
  "rayon",
  "smallvec",
 ]
 
+[[package]]
+name = "static_assertions"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
+
 [[package]]
 name = "statrs"
 version = "0.16.0"
@@ -1531,21 +1586,21 @@ dependencies = [
 
 [[package]]
 name = "strsim"
-version = "0.10.0"
+version = "0.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623"
+checksum = "5ee073c9e4cd00e28217186dbe12796d692868f432bf2e97ee73bed0c56dfa01"
 
 [[package]]
 name = "strum_macros"
-version = "0.24.3"
+version = "0.25.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1e385be0d24f186b4ce2f9982191e7101bb737312ad61c1f2f984f34bcf85d59"
+checksum = "23dc1fa9ac9c169a78ba62f0b841814b7abae11bdd047b9c58f893439e309ea0"
 dependencies = [
  "heck",
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 1.0.109",
+ "syn 2.0.52",
 ]
 
 [[package]]
@@ -1561,9 +1616,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.22"
+version = "2.0.52"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2efbeae7acf4eabd6bcdcbd11c92f45231ddda7539edc7806bd1a04a03b24616"
+checksum = "b699d15b36d1f02c3e7c69f8ffef53de37aefae075d8488d4ba1a7788d574a07"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1589,9 +1644,9 @@ dependencies = [
 
 [[package]]
 name = "terminal_size"
-version = "0.2.6"
+version = "0.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8e6bf6f19e9f8ed8d4048dc22981458ebcf406d67e94cd422e5ecd73d63b3237"
+checksum = "21bebf2b7c9e0a515f6e0f8c51dc0f8e4696391e6f1ff30379559f8365fb0df7"
 dependencies = [
  "rustix",
  "windows-sys 0.48.0",
@@ -1599,29 +1654,29 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.40"
+version = "1.0.57"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "978c9a314bd8dc99be594bc3c175faaa9794be04a5a5e153caba6915336cebac"
+checksum = "1e45bcbe8ed29775f228095caf2cd67af7a4ccf756ebff23a306bf3e8b47b24b"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.40"
+version = "1.0.57"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f9456a42c5b0d803c8cd86e73dd7cc9edd429499f37a3550d286d5e86720569f"
+checksum = "a953cb265bef375dae3de6663da4d3804eee9682ea80d8e2542529b73c531c81"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.22",
+ "syn 2.0.52",
 ]
 
 [[package]]
 name = "thread_local"
-version = "1.1.7"
+version = "1.1.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3fdd6f064ccff2d6567adcb3873ca630700f00b5ad3f060c25b5dcfd9a4ce152"
+checksum = "8b9ef9bad013ada3808854ceac7b46812a6465ba368859a37e2100283d2d719c"
 dependencies = [
  "cfg-if",
  "once_cell",
@@ -1629,24 +1684,14 @@ dependencies = [
 
 [[package]]
 name = "time"
-version = "0.1.45"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1b797afad3f312d1c66a56d11d0316f916356d11bd158fbc6ca6389ff6bf805a"
-dependencies = [
- "libc",
- "wasi 0.10.0+wasi-snapshot-preview1",
- "winapi",
-]
-
-[[package]]
-name = "time"
-version = "0.3.22"
+version = "0.3.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ea9e1b3cf1243ae005d9e74085d4d542f3125458f3a81af210d901dcd7411efd"
+checksum = "c8248b6521bb14bc45b4067159b9b6ad792e2d6d754d6c41fb50e29fefe38749"
 dependencies = [
+ "deranged",
  "itoa",
- "libc",
- "num_threads",
+ "num-conv",
+ "powerfmt",
  "serde",
  "time-core",
  "time-macros",
@@ -1654,34 +1699,20 @@ dependencies = [
 
 [[package]]
 name = "time-core"
-version = "0.1.1"
+version = "0.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7300fbefb4dadc1af235a9cef3737cea692a9d97e1b9cbcd4ebdae6f8868e6fb"
+checksum = "ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3"
 
 [[package]]
 name = "time-macros"
-version = "0.2.9"
+version = "0.2.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "372950940a5f07bf38dbe211d7283c9e6d7327df53794992d293e534c733d09b"
+checksum = "7ba3a3ef41e6672a2f0f001392bb5dcd3ff0a9992d618ca761a11c3121547774"
 dependencies = [
+ "num-conv",
  "time-core",
 ]
 
-[[package]]
-name = "tinyvec"
-version = "1.6.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50"
-dependencies = [
- "tinyvec_macros",
-]
-
-[[package]]
-name = "tinyvec_macros"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
-
 [[package]]
 name = "trait-set"
 version = "0.3.0"
@@ -1695,58 +1726,41 @@ dependencies = [
 
 [[package]]
 name = "typed-builder"
-version = "0.14.0"
+version = "0.18.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "64cba322cb9b7bc6ca048de49e83918223f35e7a86311267013afff257004870"
+checksum = "444d8748011b93cb168770e8092458cb0f8854f931ff82fdf6ddfbd72a9c933e"
 dependencies = [
- "proc-macro2",
- "quote",
- "syn 1.0.109",
+ "typed-builder-macro",
 ]
 
 [[package]]
-name = "typenum"
-version = "1.16.0"
+name = "typed-builder-macro"
+version = "0.18.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "497961ef93d974e23eb6f433eb5fe1b7930b659f06d12dec6fc44a8f554c0bba"
+checksum = "563b3b88238ec95680aef36bdece66896eaa7ce3c0f1b4f39d38fb2435261352"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.52",
+]
 
 [[package]]
-name = "unicode-bidi"
-version = "0.3.13"
+name = "typenum"
+version = "1.17.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460"
+checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
 
 [[package]]
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-version = "1.0.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0"
-
-[[package]]
-name = "unicode-normalization"
-version = "0.1.22"
+version = "1.0.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921"
-dependencies = [
- "tinyvec",
-]
+checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
 
 [[package]]
 name = "unicode-width"
-version = "0.1.10"
+version = "0.1.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c0edd1e5b14653f783770bce4a4dabb4a5108a5370a5f5d8cfe8710c361f6c8b"
-
-[[package]]
-name = "url"
-version = "2.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "50bff7831e19200a85b17131d085c25d7811bc4e186efdaf54bbd132994a88cb"
-dependencies = [
- "form_urlencoded",
- "idna",
- "percent-encoding",
-]
+checksum = "e51733f11c9c4f72aa0c160008246859e340b00807569a0da0e7a1079b27ba85"
 
 [[package]]
 name = "utf8parse"
@@ -1754,24 +1768,12 @@ version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
 
-[[package]]
-name = "vcpkg"
-version = "0.2.15"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
-
 [[package]]
 name = "version_check"
 version = "0.9.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
 
-[[package]]
-name = "wasi"
-version = "0.10.0+wasi-snapshot-preview1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1a143597ca7c7793eff794def352d41792a93c481eb1042423ff7ff72ba2c31f"
-
 [[package]]
 name = "wasi"
 version = "0.11.0+wasi-snapshot-preview1"
@@ -1780,9 +1782,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.87"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7706a72ab36d8cb1f80ffbf0e071533974a60d0a308d01a5d0375bf60499a342"
+checksum = "4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8"
 dependencies = [
  "cfg-if",
  "wasm-bindgen-macro",
@@ -1790,24 +1792,24 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-backend"
-version = "0.2.87"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ef2b6d3c510e9625e5fe6f509ab07d66a760f0885d858736483c32ed7809abd"
+checksum = "614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da"
 dependencies = [
  "bumpalo",
  "log",
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.22",
+ "syn 2.0.52",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.87"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dee495e55982a3bd48105a7b947fd2a9b4a8ae3010041b9e0faab3f9cd028f1d"
+checksum = "a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726"
 dependencies = [
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  "wasm-bindgen-macro-support",
@@ -1815,28 +1817,28 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.87"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b"
+checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.22",
+ "syn 2.0.52",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.87"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ca6ad05a4870b2bf5fe995117d3728437bd27d7cd5f06f13c17443ef369775a1"
+checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96"
 
 [[package]]
 name = "wide"
-version = "0.7.10"
+version = "0.7.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "40018623e2dba2602a9790faba8d33f2ebdebf4b86561b83928db735f8784728"
+checksum = "89beec544f246e679fc25490e3f8e08003bc4bf612068f325120dad4cea02c1c"
 dependencies = [
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  "safe_arch",
@@ -1865,145 +1867,145 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
 
 [[package]]
-name = "windows"
-version = "0.48.0"
+name = "windows-core"
+version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e686886bc078bc1b0b600cac0147aadb815089b6e4da64016cbd754b6342700f"
+checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
 dependencies = [
- "windows-targets 0.48.1",
+ "windows-targets 0.52.4",
 ]
 
 [[package]]
 name = "windows-sys"
-version = "0.45.0"
+version = "0.48.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0"
+checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9"
 dependencies = [
- "windows-targets 0.42.2",
+ "windows-targets 0.48.5",
 ]
 
 [[package]]
 name = "windows-sys"
-version = "0.48.0"
+version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9"
+checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
 dependencies = [
- "windows-targets 0.48.1",
+ "windows-targets 0.52.4",
 ]
 
 [[package]]
 name = "windows-targets"
-version = "0.42.2"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071"
+checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
 dependencies = [
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- "windows_i686_msvc 0.42.2",
- "windows_x86_64_gnu 0.42.2",
- "windows_x86_64_gnullvm 0.42.2",
- "windows_x86_64_msvc 0.42.2",
+ "windows_aarch64_gnullvm 0.48.5",
+ "windows_aarch64_msvc 0.48.5",
+ "windows_i686_gnu 0.48.5",
+ "windows_i686_msvc 0.48.5",
+ "windows_x86_64_gnu 0.48.5",
+ "windows_x86_64_gnullvm 0.48.5",
+ "windows_x86_64_msvc 0.48.5",
 ]
 
 [[package]]
 name = "windows-targets"
-version = "0.48.1"
+version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "05d4b17490f70499f20b9e791dcf6a299785ce8af4d709018206dc5b4953e95f"
+checksum = "7dd37b7e5ab9018759f893a1952c9420d060016fc19a472b4bb20d1bdd694d1b"
 dependencies = [
- "windows_aarch64_gnullvm 0.48.0",
- "windows_aarch64_msvc 0.48.0",
- "windows_i686_gnu 0.48.0",
- "windows_i686_msvc 0.48.0",
- "windows_x86_64_gnu 0.48.0",
- "windows_x86_64_gnullvm 0.48.0",
- "windows_x86_64_msvc 0.48.0",
+ "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",
 ]
 
 [[package]]
 name = "windows_aarch64_gnullvm"
-version = "0.42.2"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8"
+checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
 
 [[package]]
 name = "windows_aarch64_gnullvm"
-version = "0.48.0"
+version = "0.52.4"
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-checksum = "91ae572e1b79dba883e0d315474df7305d12f569b400fcf90581b06062f7e1bc"
+checksum = "bcf46cf4c365c6f2d1cc93ce535f2c8b244591df96ceee75d8e83deb70a9cac9"
 
 [[package]]
 name = "windows_aarch64_msvc"
-version = "0.42.2"
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-checksum = "e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43"
+checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
 
 [[package]]
 name = "windows_aarch64_msvc"
-version = "0.48.0"
+version = "0.52.4"
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-checksum = "b2ef27e0d7bdfcfc7b868b317c1d32c641a6fe4629c171b8928c7b08d98d7cf3"
+checksum = "da9f259dd3bcf6990b55bffd094c4f7235817ba4ceebde8e6d11cd0c5633b675"
 
 [[package]]
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-version = "0.42.2"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f"
+checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
 
 [[package]]
 name = "windows_i686_gnu"
-version = "0.48.0"
+version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "622a1962a7db830d6fd0a69683c80a18fda201879f0f447f065a3b7467daa241"
+checksum = "b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3"
 
 [[package]]
 name = "windows_i686_msvc"
-version = "0.42.2"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060"
+checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
 
 [[package]]
 name = "windows_i686_msvc"
-version = "0.48.0"
+version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4542c6e364ce21bf45d69fdd2a8e455fa38d316158cfd43b3ac1c5b1b19f8e00"
+checksum = "1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02"
 
 [[package]]
 name = "windows_x86_64_gnu"
-version = "0.42.2"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36"
+checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
 
 [[package]]
 name = "windows_x86_64_gnu"
-version = "0.48.0"
+version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ca2b8a661f7628cbd23440e50b05d705db3686f894fc9580820623656af974b1"
+checksum = "5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
-version = "0.42.2"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3"
+checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
-version = "0.48.0"
+version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7896dbc1f41e08872e9d5e8f8baa8fdd2677f29468c4e156210174edc7f7b953"
+checksum = "77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177"
 
 [[package]]
 name = "windows_x86_64_msvc"
-version = "0.42.2"
+version = "0.48.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0"
+checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
 
 [[package]]
 name = "windows_x86_64_msvc"
-version = "0.48.0"
+version = "0.52.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a"
+checksum = "32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8"
 
 [[package]]
 name = "xz2"
@@ -2013,3 +2015,23 @@ checksum = "388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2"
 dependencies = [
  "lzma-sys",
 ]
+
+[[package]]
+name = "zerocopy"
+version = "0.7.32"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be"
+dependencies = [
+ "zerocopy-derive",
+]
+
+[[package]]
+name = "zerocopy-derive"
+version = "0.7.32"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.52",
+]
diff --git a/Cargo.toml b/Cargo.toml
index a69f6cf..eeefa95 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "alevin-fry"
-version = "0.8.2"
+version = "0.9.0"
 authors = [
   "Avi Srivastava <avi.srivastava@nyu.edu>",
   "Hirak Sarkar <hirak_sarkar@hms.harvard.edu>",
@@ -32,56 +32,73 @@ keywords = [
 ]
 categories = ["command-line-utilities", "science"]
 
-[workspace]
-
 [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 = "0.6.0" }
-anyhow = "1.0.71"
+libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.8.2" }
+anyhow = "1.0.80"
 arrayvec = "0.7.4"
-ahash = "0.8.3"
+ahash = "0.8.11"
 bincode = "1.3.3"
-bstr = "1.5.0"
-crossbeam-channel = "0.5.8"
-crossbeam-queue = "0.3.8"
-# derive_builder = "0.11.2"
-typed-builder = "0.14.0"
-indicatif = "0.17.5"
+bstr = "1.9.1"
+crossbeam-channel = "0.5.12"
+crossbeam-queue = "0.3.11"
+typed-builder = "0.18.1"
+indicatif = "0.17.8"
 needletail = "0.5.1"
-petgraph = "0.6.3"
-flate2 = "1.0.26"
-scroll = "0.11.0"
-serde = { version = "1.0.164", features = ["derive"] }
-serde_json = "1.0.99"
+petgraph = "0.6.4"
+flate2 = "1.0.28"
+scroll = "0.12.0"
+serde = { version = "1.0.197", features = ["derive"] }
+serde_json = "1.0.114"
 sprs = "0.11.1"
 slog = "2.7.0"
-slog-term = "2.9.0"
-slog-async = "2.7.0"
-smallvec = "1.10.0"
-snap = "1.1.0"
+slog-term = "2.9.1"
+slog-async = "2.8.0"
+smallvec = "1.13.1"
+snap = "1.1.1"
 rand = "0.8.5"
-chrono = "0.4.26"
-csv = "1.2.2"
-mimalloc = { version = "0.1.37", default-features = false }
+chrono = "0.4.35"
+csv = "1.3.0"
+mimalloc = { version = "0.1.39", default-features = false }
 num-format = "0.4.4"
 num_cpus = "1.16.0"
-bio-types = { version = "1.0.0", default-features = true, features = ["serde"] }
-itertools = "0.11.0"
-thiserror = "1.0.40"
+bio-types = { version = "1.0.1", default-features = true, features = ["serde"] }
+itertools = "0.12.1"
+thiserror = "1.0.57"
 statrs = "0.16.0"
-rust-htslib = { version = "0.44.1", default-features = false, features = [
-  "bzip2",
-  "lzma",
-] }
 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 = "=4.3.9", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] }
+clap = { version = "=4.5.2", 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"] }
 
 [profile.release]
 #debug = true
 lto = "thin"
 #codegen-units=1
 opt-level = 3
+
+# The profile that 'cargo dist' will build with
+[profile.dist]
+inherits = "release"
+lto = "thin"
+
+# Config for 'cargo dist'
+[workspace.metadata.dist]
+# The preferred cargo-dist version to use in CI (Cargo.toml SemVer syntax)
+cargo-dist-version = "0.11.1"
+# CI backends to support
+ci = ["github"]
+# The installers to generate for each app
+installers = ["shell"]
+# Target platforms to build apps for (Rust target-triple syntax)
+targets = ["aarch64-apple-darwin", "x86_64-apple-darwin", "x86_64-unknown-linux-gnu"]
+# Publish jobs to run in CI
+pr-run-mode = "plan"
+
+[workspace.metadata.dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"
diff --git a/docs/source/overview.rst b/docs/source/overview.rst
index d3d638f..37fa9a2 100644
--- a/docs/source/overview.rst
+++ b/docs/source/overview.rst
@@ -3,7 +3,7 @@ Overview
 
 `alevin-fry`` is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data. It consumes RAD files generated by `salmon alevin`, and performs common operations like generating permit lists, and estimating the number of distinct molecules from each gene within each cell. The focus in `alevin-fry`` is on safety, accuracy and efficiency (in terms of both time and memory usage).
 
-You can read the paper describing alevin fry, "Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data" [here](https://www.nature.com/articles/s41592-022-01408-3), and the pre-print [on bioRxiv](https://www.biorxiv.org/content/10.1101/2021.06.29.450377v1).
+You can read the paper describing alevin fry, "Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data" `here <https://www.nature.com/articles/s41592-022-01408-3>`_, and the pre-print `on bioRxiv <https://www.biorxiv.org/content/10.1101/2021.06.29.450377v1>`_.
 
 Other resources for alevin-fry
 ==============================
diff --git a/scripts/bsd-3.tmpl b/scripts/bsd-3.tmpl
new file mode 100644
index 0000000..2828051
--- /dev/null
+++ b/scripts/bsd-3.tmpl
@@ -0,0 +1,6 @@
+Copyright (c) ${years} ${owner}.
+
+This file is part of ${projectname}
+(see ${projecturl}).
+
+License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
diff --git a/scripts/reheader.sh b/scripts/reheader.sh
new file mode 100755
index 0000000..5c99dcd
--- /dev/null
+++ b/scripts/reheader.sh
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+if ! command -v licenseheaders &> /dev/null
+then
+    echo "licenseheaders could not be found; please install this program to use the script (pip install licenseheaders)."
+    exit 1
+fi
+
+
+licenseheaders -d ../src -y 2020-2024 -t bsd-3.tmpl -o COMBINE-lab -n alevin-fry -u https://www.github.com/COMBINE-lab/alevin-fry -D -E rs
diff --git a/src/cellfilter.rs b/src/cellfilter.rs
index 98d83b9..a9131fd 100644
--- a/src/cellfilter.rs
+++ b/src/cellfilter.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
@@ -19,8 +19,13 @@ use bio_types::strand::Strand;
 use bstr::io::BufReadExt;
 use itertools::Itertools;
 use libradicl::exit_codes;
-use libradicl::rad_types;
+use libradicl::rad_types::{self, RadType};
 use libradicl::BarcodeLookupMap;
+use libradicl::{
+    chunk,
+    header::RadPrelude,
+    record::{AlevinFryReadRecord, AlevinFryRecordContext},
+};
 use needletail::bitkmer::*;
 use num_format::{Locale, ToFormattedString};
 use serde::Serialize;
@@ -222,7 +227,7 @@ fn populate_unfiltered_barcode_map<T: Read>(
 fn process_unfiltered(
     mut hm: HashMap<u64, u64, ahash::RandomState>,
     mut unmatched_bc: Vec<u64>,
-    ft_vals: &rad_types::FileTags,
+    file_tag_map: &rad_types::TagMap,
     filter_meth: &CellFilterMethod,
     expected_ori: Strand,
     output_dir: &PathBuf,
@@ -279,9 +284,14 @@ fn process_unfiltered(
         num_passing.to_formatted_string(&Locale::en)
     );
 
+    let barcode_tag = file_tag_map
+        .get("cblen")
+        .expect("tag map must contain cblen");
+    let barcode_len: u16 = barcode_tag.try_into()?;
+
     // now, we create a second barcode map with just the barcodes
     // for cells we will keep / rescue.
-    let bcmap2 = BarcodeLookupMap::new(kept_bc, ft_vals.bclen as u32);
+    let bcmap2 = BarcodeLookupMap::new(kept_bc, barcode_len as u32);
     info!(
         log,
         "found {} cells with non-trivial number of reads by exact barcode match",
@@ -382,7 +392,7 @@ fn process_unfiltered(
     })?;
     let o_path = parent.join("permit_freq.bin");
 
-    match afutils::write_permit_list_freq(&o_path, ft_vals.bclen, &hm) {
+    match afutils::write_permit_list_freq(&o_path, barcode_len, &hm) {
         Ok(_) => {}
         Err(error) => {
             panic!("Error: {}", error);
@@ -444,7 +454,7 @@ fn process_unfiltered(
 #[allow(clippy::unnecessary_unwrap, clippy::too_many_arguments)]
 fn process_filtered(
     hm: &HashMap<u64, u64, ahash::RandomState>,
-    ft_vals: &rad_types::FileTags,
+    file_tag_map: &rad_types::TagMap,
     filter_meth: &CellFilterMethod,
     expected_ori: Strand,
     output_dir: &PathBuf,
@@ -460,6 +470,11 @@ fn process_filtered(
     freq.sort_unstable();
     freq.reverse();
 
+    let barcode_tag = file_tag_map
+        .get("cblen")
+        .expect("tag map must contain cblen");
+    let barcode_len: u16 = barcode_tag.try_into()?;
+
     // select from among supported filter methods
     match filter_meth {
         CellFilterMethod::KneeFinding => {
@@ -489,7 +504,7 @@ fn process_filtered(
             valid_bc = permit_list_from_threshold(hm, min_freq);
         }
         CellFilterMethod::ExplicitList(valid_bc_file) => {
-            valid_bc = permit_list_from_file(valid_bc_file, ft_vals.bclen);
+            valid_bc = permit_list_from_file(valid_bc_file, barcode_len);
         }
         CellFilterMethod::ExpectCells(expected_num_cells) => {
             let robust_quantile = 0.99f64;
@@ -509,7 +524,7 @@ fn process_filtered(
     // generate the map from each permitted barcode to all barcodes within
     // edit distance 1 of it.
     let full_permit_list =
-        afutils::generate_permitlist_map(&valid_bc, ft_vals.bclen as usize).unwrap();
+        afutils::generate_permitlist_map(&valid_bc, barcode_len as usize).unwrap();
 
     let s2 = ahash::RandomState::with_seeds(2u64, 7u64, 1u64, 8u64);
     let mut permitted_map = HashMap::with_capacity_and_hasher(valid_bc.len(), s2);
@@ -532,7 +547,7 @@ fn process_filtered(
     })?;
     let o_path = parent.join("permit_freq.bin");
 
-    match afutils::write_permit_list_freq(&o_path, ft_vals.bclen, &permitted_map) {
+    match afutils::write_permit_list_freq(&o_path, barcode_len, &permitted_map) {
         Ok(_) => {}
         Err(error) => {
             panic!("Error: {}", error);
@@ -541,7 +556,7 @@ fn process_filtered(
 
     let o_path = parent.join("all_freq.bin");
 
-    match afutils::write_permit_list_freq(&o_path, ft_vals.bclen, hm) {
+    match afutils::write_permit_list_freq(&o_path, barcode_len, hm) {
         Ok(_) => {}
         Err(error) => {
             panic!("Error: {}", error);
@@ -630,7 +645,9 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
 
     let i_file = File::open(i_dir.join("map.rad")).context("could not open input rad file")?;
     let mut br = BufReader::new(i_file);
-    let hdr = rad_types::RadHeader::from_bytes(&mut br);
+
+    let prelude = RadPrelude::from_bytes(&mut br)?;
+    let hdr = &prelude.hdr;
     info!(
         log,
         "paired : {:?}, ref_count : {}, num_chunks : {}",
@@ -638,24 +655,25 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
         hdr.ref_count.to_formatted_string(&Locale::en),
         hdr.num_chunks.to_formatted_string(&Locale::en)
     );
+
     // file-level
-    let fl_tags = rad_types::TagSection::from_bytes(&mut br);
+    let fl_tags = &prelude.file_tags;
     info!(log, "read {:?} file-level tags", fl_tags.tags.len());
     // read-level
-    let rl_tags = rad_types::TagSection::from_bytes(&mut br);
+    let rl_tags = &prelude.read_tags;
     info!(log, "read {:?} read-level tags", rl_tags.tags.len());
 
     // right now, we only handle BC and UMI types of U8—U64, so validate that
     const BNAME: &str = "b";
     const UNAME: &str = "u";
 
-    let mut bct: Option<u8> = None;
-    let mut umit: Option<u8> = None;
+    let mut bct: Option<RadType> = None;
+    let mut umit: Option<RadType> = None;
 
     for rt in &rl_tags.tags {
         // if this is one of our tags
         if rt.name == BNAME || rt.name == UNAME {
-            if rad_types::decode_int_type_tag(rt.typeid).is_none() {
+            if !rt.typeid.is_int_type() {
                 crit!(
                     log,
                     "currently only RAD types 1--4 are supported for 'b' and 'u' tags."
@@ -671,21 +689,19 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
             }
         }
     }
+    assert!(bct.is_some(), "barcode type tag must be present.");
+    assert!(umit.is_some(), "umi type tag must be present.");
 
     // alignment-level
-    let al_tags = rad_types::TagSection::from_bytes(&mut br);
+    let al_tags = &prelude.aln_tags;
     info!(log, "read {:?} alignemnt-level tags", al_tags.tags.len());
 
-    let ft_vals = rad_types::FileTags::from_bytes(&mut br);
-    info!(log, "File-level tag values {:?}", ft_vals);
+    let file_tag_map = prelude.file_tags.parse_tags_from_bytes(&mut br)?;
+    info!(log, "File-level tag values {:?}", file_tag_map);
 
+    let record_context = prelude.get_record_context::<AlevinFryRecordContext>()?;
     let mut num_reads: usize = 0;
 
-    let bc_type = rad_types::decode_int_type_tag(bct.expect("no barcode tag description present."))
-        .context("unknown barcode type id.")?;
-    let umi_type = rad_types::decode_int_type_tag(umit.expect("no umi tag description present"))
-        .context("unknown barcode type id.")?;
-
     // if dealing with filtered type
     let s = ahash::RandomState::with_seeds(2u64, 7u64, 1u64, 8u64);
     let mut hm = HashMap::with_hasher(s);
@@ -702,7 +718,8 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
             // the unfiltered_bc_count map must be valid in this branch
             if let Some(mut hmu) = unfiltered_bc_counts {
                 for _ in 0..(hdr.num_chunks as usize) {
-                    let c = rad_types::Chunk::from_bytes(&mut br, &bc_type, &umi_type);
+                    let c =
+                        chunk::Chunk::<AlevinFryReadRecord>::from_bytes(&mut br, &record_context);
                     num_orientation_compat_reads += update_barcode_hist_unfiltered(
                         &mut hmu,
                         &mut unmatched_bc,
@@ -723,7 +740,7 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
                 process_unfiltered(
                     hmu,
                     unmatched_bc,
-                    &ft_vals,
+                    &file_tag_map,
                     &filter_meth,
                     expected_ori,
                     output_dir,
@@ -740,7 +757,7 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
         }
         _ => {
             for _ in 0..(hdr.num_chunks as usize) {
-                let c = rad_types::Chunk::from_bytes(&mut br, &bc_type, &umi_type);
+                let c = chunk::Chunk::<AlevinFryReadRecord>::from_bytes(&mut br, &record_context);
                 update_barcode_hist(&mut hm, &mut max_ambiguity_read, &c, &expected_ori);
                 num_reads += c.reads.len();
             }
@@ -753,7 +770,7 @@ pub fn generate_permit_list(gpl_opts: GenPermitListOpts) -> anyhow::Result<u64>
             );
             process_filtered(
                 &hm,
-                &ft_vals,
+                &file_tag_map,
                 &filter_meth,
                 expected_ori,
                 output_dir,
@@ -900,7 +917,7 @@ pub fn update_barcode_hist_unfiltered(
     hist: &mut HashMap<u64, u64, ahash::RandomState>,
     unmatched_bc: &mut Vec<u64>,
     max_ambiguity_read: &mut usize,
-    chunk: &rad_types::Chunk,
+    chunk: &chunk::Chunk<AlevinFryReadRecord>,
     expected_ori: &Strand,
 ) -> usize {
     let mut num_strand_compat_reads = 0usize;
@@ -964,7 +981,7 @@ pub fn update_barcode_hist_unfiltered(
 pub fn update_barcode_hist(
     hist: &mut HashMap<u64, u64, ahash::RandomState>,
     max_ambiguity_read: &mut usize,
-    chunk: &rad_types::Chunk,
+    chunk: &chunk::Chunk<AlevinFryReadRecord>,
     expected_ori: &Strand,
 ) {
     match expected_ori {
diff --git a/src/cmd_parse_utils.rs b/src/cmd_parse_utils.rs
index dd66ce2..c947ac5 100644
--- a/src/cmd_parse_utils.rs
+++ b/src/cmd_parse_utils.rs
@@ -1,3 +1,11 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
 use crate::quant::{ResolutionStrategy, SplicedAmbiguityModel};
 use clap;
 use std::path::{Path, PathBuf};
diff --git a/src/collate.rs b/src/collate.rs
index 40be896..d296fd1 100644
--- a/src/collate.rs
+++ b/src/collate.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
@@ -16,8 +16,13 @@ use crate::utils::InternalVersionInfo;
 use bio_types::strand::{Strand, StrandError};
 use crossbeam_queue::ArrayQueue;
 // use dashmap::DashMap;
+
+use libradicl::chunk;
+use libradicl::header::{RadHeader, RadPrelude};
 use libradicl::rad_types;
+use libradicl::record::AlevinFryReadRecord;
 use libradicl::schema::TempCellInfo;
+
 use num_format::{Locale, ToFormattedString};
 use scroll::{Pread, Pwrite};
 use serde_json::json;
@@ -118,7 +123,7 @@ where
     let freq_hm: HashMap<u64, u64> =
         bincode::deserialize_from(rdr).context("couldn't deserialize barcode to frequency map.")?;
     let total_to_collate = freq_hm.values().sum();
-    let mut tsv_map = Vec::from_iter(freq_hm.into_iter());
+    let mut tsv_map = Vec::from_iter(freq_hm);
 
     // sort this so that we deal with largest cells (by # of reads) first
     // sort in _descending_ order by count.
@@ -365,7 +370,7 @@ where
     let i_file = File::open(&input_rad_path).context("couldn't open input RAD file")?;
     let mut br = BufReader::new(i_file);
 
-    let hdr = rad_types::RadHeader::from_bytes(&mut br);
+    let hdr = RadHeader::from_bytes(&mut br)?;
 
     // the exact position at the end of the header,
     // precisely sizeof(u64) bytes beyond the num_chunks field.
@@ -381,17 +386,22 @@ where
     );
 
     // file-level
-    let fl_tags = rad_types::TagSection::from_bytes(&mut br);
+    let fl_tags = rad_types::TagSection::from_bytes(&mut br)?;
     info!(log, "read {:?} file-level tags", fl_tags.tags.len());
     // read-level
-    let rl_tags = rad_types::TagSection::from_bytes(&mut br);
+    let rl_tags = rad_types::TagSection::from_bytes(&mut br)?;
     info!(log, "read {:?} read-level tags", rl_tags.tags.len());
     // alignment-level
-    let al_tags = rad_types::TagSection::from_bytes(&mut br);
+    let al_tags = rad_types::TagSection::from_bytes(&mut br)?;
     info!(log, "read {:?} alignemnt-level tags", al_tags.tags.len());
 
-    let ft_vals = rad_types::FileTags::from_bytes(&mut br);
-    info!(log, "File-level tag values {:?}", ft_vals);
+    // create the prelude and rebind the variables we need
+    let prelude = RadPrelude::from_header_and_tag_sections(hdr, fl_tags, rl_tags, al_tags);
+    let hdr = &prelude.hdr;
+    let rl_tags = &prelude.read_tags;
+
+    let file_tag_map = prelude.file_tags.parse_tags_from_bytes(&mut br);
+    info!(log, "File-level tag values {:?}", file_tag_map);
 
     let bct = rl_tags.tags[0].typeid;
     let umit = rl_tags.tags[1].typeid;
@@ -456,10 +466,10 @@ where
         correct_map.len().to_formatted_string(&Locale::en)
     );
 
-    let cc = rad_types::ChunkConfig {
+    let cc = chunk::ChunkConfig {
         num_chunks: hdr.num_chunks,
-        bc_type: bct,
-        umi_type: umit,
+        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"),
     };
 
     // TODO: see if we can do this without the Arc
@@ -631,7 +641,7 @@ where
     // worker threads.
     let mut buf = vec![0u8; 65536];
     for cell_num in 0..(cc.num_chunks as usize) {
-        let (nbytes_chunk, nrec_chunk) = rad_types::Chunk::read_header(&mut br);
+        let (nbytes_chunk, nrec_chunk) = chunk::Chunk::<AlevinFryReadRecord>::read_header(&mut br);
         buf.resize(nbytes_chunk as usize, 0);
         buf.pwrite::<u32>(nbytes_chunk, 0)?;
         buf.pwrite::<u32>(nrec_chunk, 4)?;
@@ -720,7 +730,7 @@ where
         let bc_type =
             rad_types::decode_int_type_tag(cc.bc_type).context("unknown barcode type id.")?;
         let umi_type =
-            rad_types::decode_int_type_tag(cc.umi_type).context("unknown barcode type id.")?;
+            rad_types::decode_int_type_tag(cc.umi_type).context("unknown umi type id.")?;
         // have access to the input directory
         let input_dir: PathBuf = input_dir.clone();
         // the output file
diff --git a/src/constants.rs b/src/constants.rs
index 9443bf6..9a4ad7a 100644
--- a/src/constants.rs
+++ b/src/constants.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
diff --git a/src/convert.rs b/src/convert.rs
index 47fe434..4247f7d 100644
--- a/src/convert.rs
+++ b/src/convert.rs
@@ -1,27 +1,37 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
 
-use anyhow::Context;
+use anyhow::bail;
 use indicatif::{ProgressBar, ProgressStyle};
 use slog::{crit, info};
+
 //use num_format::{Locale};
 use std::fs;
 use std::fs::File;
 use std::io::{stdout, BufReader, BufWriter, Cursor, Seek, SeekFrom, Write};
 // use std::sync::{Arc, Mutex};
-use libradicl::rad_types;
+//
+
+use noodles::bam as nbam;
+use noodles::{bgzf, sam};
+use sam::alignment::record::data::field::{tag::Tag as SamTag, value::Value as SamTagValue};
+
+use libradicl::rad_types::{self, RadIntId, RadType, TagDesc, TagSection, TagSectionLabel};
 use libradicl::utils::MASK_LOWER_31_U32;
+use libradicl::{
+    chunk,
+    header::{RadHeader, RadPrelude},
+    record::{AlevinFryReadRecord, AlevinFryRecordContext},
+};
+
 use needletail::bitkmer::*;
 use rand::Rng;
-use rust_htslib::bam::HeaderView;
-use rust_htslib::{bam, bam::record::Aux, bam::Read};
-use std::collections::HashMap;
 use std::error::Error;
 use std::path::Path;
 use std::str;
@@ -42,7 +52,7 @@ use std::str;
 
 #[allow(dead_code)]
 fn get_random_nucl() -> &'static str {
-    let nucl = vec!["A", "T", "G", "C"];
+    let nucl = ["A", "T", "G", "C"];
     let mut rng = rand::thread_rng();
     let idx = rng.gen_range(0..4);
     nucl[idx]
@@ -78,25 +88,68 @@ pub fn cb_string_to_u64(cb_str: &[u8]) -> Result<u64, Box<dyn Error>> {
     Ok(cb_id)
 }
 
-#[allow(dead_code)]
-pub fn tid_2_contig(h: &HeaderView) -> HashMap<u32, String> {
-    let mut dict: HashMap<u32, String> = HashMap::with_capacity(46);
-    for (i, t) in h
-        .target_names()
-        .iter()
-        .map(|a| str::from_utf8(a).unwrap())
-        .enumerate()
-    {
-        dict.insert(i as u32, t.to_owned());
+#[inline]
+fn write_barcode<W: Write>(barcode_t: &RadType, barcode: u64, w: &mut W) -> anyhow::Result<()> {
+    match barcode_t {
+        RadType::Int(int_t) => match int_t {
+            RadIntId::U8 => {
+                let v = barcode as u8;
+                w.write_all(&v.to_le_bytes())?;
+            }
+            RadIntId::U16 => {
+                let v = barcode as u16;
+                w.write_all(&v.to_le_bytes())?;
+            }
+            RadIntId::U32 => {
+                let v = barcode as u32;
+                w.write_all(&v.to_le_bytes())?;
+            }
+            RadIntId::U64 => {
+                let v = barcode;
+                w.write_all(&v.to_le_bytes())?;
+            }
+        },
+        _ => bail!("invalid type!"),
+    }
+    Ok(())
+}
+
+#[inline]
+fn write_list<W: Write>(
+    tid_list: &[u32],
+    bct: &RadType,
+    bc: u64,
+    umit: &RadType,
+    umi: u64,
+    w: &mut W,
+) -> anyhow::Result<()> {
+    assert!(!tid_list.is_empty(), "Trying to write empty tid_list");
+    let na = tid_list.len() as u32;
+    w.write_all(&na.to_le_bytes()).unwrap();
+    //bc
+    write_barcode(bct, bc, w)?;
+    //umi
+    write_barcode(umit, umi, w)?;
+    //write tid list
+    for t in tid_list.iter() {
+        w.write_all(&t.to_le_bytes()).unwrap();
     }
-    dict
+    Ok(())
 }
 
-pub fn bam2rad<P1, P2>(input_file: P1, rad_file: P2, num_threads: u32, log: &slog::Logger)
+pub fn bam2rad<P1, P2>(
+    input_file: P1,
+    rad_file: P2,
+    num_threads: u32,
+    log: &slog::Logger,
+) -> anyhow::Result<()>
 where
     P1: AsRef<Path>,
     P2: AsRef<Path>,
 {
+    const CR: SamTag = SamTag::new(b'C', b'R');
+    const UR: SamTag = SamTag::new(b'U', b'R');
+
     let oname = Path::new(rad_file.as_ref());
     let parent = oname.parent().unwrap();
     std::fs::create_dir_all(parent).unwrap();
@@ -106,7 +159,7 @@ where
     }
     let ofile = File::create(rad_file.as_ref()).unwrap();
 
-    let mut bam = bam::Reader::from_path(&input_file).unwrap();
+    // number of bytes in the input BAM file
     let bam_bytes = fs::metadata(&input_file).unwrap().len();
     info! {
     log,
@@ -114,160 +167,172 @@ where
     bam_bytes
     };
 
-    if num_threads > 1 {
-        bam.set_threads((num_threads as usize) - 1).unwrap();
-    } else {
-        bam.set_threads(1).unwrap();
-    }
+    // reading input BAM using Noodles
+    // example from https://github.com/zaeleus/noodles/issues/227
+    let file = File::open(&input_file)?;
+
+    let mut reader: Box<dyn sam::alignment::io::Read<_>> =
+        match input_file.as_ref().extension().and_then(|ext| ext.to_str()) {
+            Some("bam") | Some("BAM") => {
+                let decomp_threads = std::num::NonZeroUsize::new(if num_threads > 1 {
+                    (num_threads - 1) as usize
+                } else {
+                    1_usize
+                })
+                .expect("invalid nonzero usize");
+
+                println!(
+                    "parsing BAM file using {:?} decompression threads",
+                    decomp_threads
+                );
 
-    let hdrv = bam.header().to_owned();
-    // let tid_lookup: HashMap<u32, String>  = tid_2_contig(&hdrv);
+                let decoder: Box<dyn std::io::BufRead> = Box::new(
+                    bgzf::MultithreadedReader::with_worker_count(decomp_threads, file),
+                );
+                Box::new(nbam::io::Reader::from(decoder))
+            }
+            Some("sam") | Some("SAM") => {
+                let inner: Box<dyn std::io::BufRead> = Box::new(BufReader::new(file));
+                Box::new(sam::io::Reader::from(inner))
+            }
+            _ => {
+                bail!("unsupported input file format, must end with bam/BAM or sam/SAM");
+            }
+        };
+
+    let hdrv = reader.read_alignment_header()?;
     let mut data = Cursor::new(vec![]);
-    // initialize the header (do we need this ?)
-    // let mut hdr = libradicl::RadHeader::from_bam_header(&hdrv);
-    // number of chunks would be decided when we know
-    // let end_header_pos2 = hdr.get_size();
-    // info!(
-    //     log,
-    //     "end header pos {:?}",
-    //     end_header_pos2,
-    // );
-
-    // file writer
-    // let owriter = Arc::new(Mutex::new(BufWriter::with_capacity(1048576, ofile)));
-    let mut owriter = BufWriter::with_capacity(1048576, ofile);
+
     // intermediate buffer
+    let mut owriter = BufWriter::with_capacity(1_048_576, ofile);
 
     // write the header
     {
-        // NOTE: This is hard-coded for unpaired single-cell data
-        // consider if we should generalize this
-        let is_paired = 0u8;
-        data.write_all(&is_paired.to_le_bytes())
-            .expect("couldn't write to output file");
-        let ref_count = hdrv.target_count() as u64;
-        data.write_all(&ref_count.to_le_bytes())
-            .expect("couldn't write to output file");
-        // create longest buffer
-        for t in hdrv.target_names().iter() {
-            let name_size = t.len() as u16;
-            data.write_all(&name_size.to_le_bytes())
-                .expect("coudn't write to output file");
-            data.write_all(t).expect("coudn't write to output file");
-        }
-        let initial_num_chunks = 0u64;
-        data.write_all(&initial_num_chunks.to_le_bytes())
-            .expect("coudn't write to output file");
+        // NOTE: The is_paired flag is not present in the
+        // SAM file and so isn't meaningful as written here.
+        // Also, the num_chunks will be 0 in this header
+        // currently.
+        let rad_header = RadHeader::from_bam_header(&hdrv);
+        rad_header.write(&mut data)?;
     }
 
     // test the header
     {
-        info!(log, "ref count: {:?} ", hdrv.target_count(),);
+        info!(log, "ref count: {:?} ", hdrv.reference_sequences().len(),);
     }
 
-    // keep a pointer to header pos
+    // keep a pointer to header pos we need this to fill in the correct
+    // number of chunks later on.
     let end_header_pos = data.stream_position().unwrap() - std::mem::size_of::<u64>() as u64;
 
     // check header position
     info!(log, "end header pos: {:?}", end_header_pos,);
 
+    let mut record_it = reader.alignment_records(&hdrv).peekable();
+
     // ### start of tags
     // get the first record for creating flags
-    let mut rec = bam::Record::new();
-    let first_record_exists = bam.read(&mut rec).is_some();
+    let rec_res = record_it.peek();
+    let first_record_exists = rec_res.is_some();
     if !first_record_exists {
         crit!(log, "bam file had no records!");
         std::process::exit(1);
     }
+    let rec = match rec_res.unwrap() {
+        Ok(x) => x.as_ref(),
+        Err(e) => bail!("{}", e),
+    };
+
+    let bc_typeid: RadType;
+    let umi_typeid: RadType;
 
+    use bstr::BStr;
     // Tags we will have
     // write the tag meta-information section
     {
         // file-level
-        let mut num_tags = 2u16;
-        data.write_all(&num_tags.to_le_bytes())
-            .expect("coudn't write to output file");
-        // type-id
-        let mut typeid = 2u8;
-        let mut cb_tag_str = "cblen";
-        let mut umi_tag_str = "ulen";
-
-        // str - type
-        rad_types::write_str_bin(cb_tag_str, &rad_types::RadIntId::U16, &mut data);
-        data.write_all(&typeid.to_le_bytes())
-            .expect("coudn't write to output file");
-
-        // str - type
-        rad_types::write_str_bin(umi_tag_str, &rad_types::RadIntId::U16, &mut data);
-        data.write_all(&typeid.to_le_bytes())
-            .expect("coudn't write to output file");
+        let mut file_tags = TagSection::new_with_label(TagSectionLabel::FileTags);
+        file_tags.add_tag_desc(TagDesc {
+            name: "cblen".to_owned(),
+            typeid: RadType::Int(RadIntId::U16),
+        });
+        file_tags.add_tag_desc(TagDesc {
+            name: "ulen".to_owned(),
+            typeid: RadType::Int(RadIntId::U16),
+        });
+
+        file_tags.write(&mut data)?;
 
         // read-level
-        let bc_string_in: &str = if let Ok(Aux::String(bcs)) = rec.aux(b"CR") {
-            bcs
+        let flag_data = rec.data();
+        let bc_string_in: &str = if let Some(Ok(bcs)) = flag_data.get(&CR) {
+            match bcs {
+                SamTagValue::String(bstr) => str::from_utf8(<BStr as AsRef<[u8]>>::as_ref(bstr))?,
+                _ => {
+                    bail!("cannot convert non-string (Z) tag into barcode string.");
+                }
+            }
         } else {
             panic!("Input record missing CR tag!")
         };
 
-        let umi_string_in: &str = if let Ok(Aux::String(umis)) = rec.aux(b"UR") {
-            umis
+        let umi_string_in: &str = if let Some(Ok(umis)) = flag_data.get(&UR) {
+            match umis {
+                SamTagValue::String(bstr) => str::from_utf8(<BStr as AsRef<[u8]>>::as_ref(bstr))?,
+                _ => {
+                    bail!("cannot convert non-string (Z) tag into umi string.");
+                }
+            }
         } else {
             panic!("Input record missing UR tag!")
         };
-
         let bclen = bc_string_in.len() as u16;
         let umilen = umi_string_in.len() as u16;
 
-        data.write_all(&num_tags.to_le_bytes())
-            .expect("coudn't write to output file");
-        cb_tag_str = "b";
-        umi_tag_str = "u";
-
         // type is conditional on barcode and umi length
-        let bc_typeid = match bclen {
-            1..=4 => rad_types::encode_type_tag(rad_types::RadType::U8).unwrap(),
-            5..=8 => rad_types::encode_type_tag(rad_types::RadType::U16).unwrap(),
-            9..=16 => rad_types::encode_type_tag(rad_types::RadType::U32).unwrap(),
-            17..=32 => rad_types::encode_type_tag(rad_types::RadType::U64).unwrap(),
+        bc_typeid = match bclen {
+            1..=4 => RadType::Int(rad_types::RadIntId::U8),
+            5..=8 => RadType::Int(rad_types::RadIntId::U16),
+            9..=16 => RadType::Int(rad_types::RadIntId::U32),
+            17..=32 => RadType::Int(rad_types::RadIntId::U64),
             l => {
                 crit!(log, "cannot encode barcode of length {} > 32", l);
                 std::process::exit(1);
             }
         };
 
-        let umi_typeid = match umilen {
-            1..=4 => rad_types::encode_type_tag(rad_types::RadType::U8).unwrap(),
-            5..=8 => rad_types::encode_type_tag(rad_types::RadType::U16).unwrap(),
-            9..=16 => rad_types::encode_type_tag(rad_types::RadType::U32).unwrap(),
-            17..=32 => rad_types::encode_type_tag(rad_types::RadType::U64).unwrap(),
+        umi_typeid = match umilen {
+            1..=4 => RadType::Int(rad_types::RadIntId::U8),
+            5..=8 => RadType::Int(rad_types::RadIntId::U16),
+            9..=16 => RadType::Int(rad_types::RadIntId::U32),
+            17..=32 => RadType::Int(rad_types::RadIntId::U64),
             l => {
                 crit!(log, "cannot encode umi of length {} > 32", l);
                 std::process::exit(1);
             }
         };
 
-        //info!(log, "CB LEN : {}, UMI LEN : {}", bclen, umilen);
-
-        rad_types::write_str_bin(cb_tag_str, &rad_types::RadIntId::U16, &mut data);
-        data.write_all(&bc_typeid.to_le_bytes())
-            .expect("coudn't write to output file");
-
-        rad_types::write_str_bin(umi_tag_str, &rad_types::RadIntId::U16, &mut data);
-        data.write_all(&umi_typeid.to_le_bytes())
-            .expect("coudn't write to output file");
+        let mut read_tags = TagSection::new_with_label(TagSectionLabel::ReadTags);
+        read_tags.add_tag_desc(TagDesc {
+            name: "b".to_owned(),
+            typeid: bc_typeid,
+        });
+        read_tags.add_tag_desc(TagDesc {
+            name: "u".to_owned(),
+            typeid: umi_typeid,
+        });
+        read_tags.write(&mut data)?;
 
         // alignment-level
-        num_tags = 1u16;
-        data.write_all(&num_tags.to_le_bytes())
-            .expect("couldn't write to output file");
-
-        // reference id
-        let refid_str = "compressed_ori_refid";
-        typeid = 3u8;
-        rad_types::write_str_bin(refid_str, &rad_types::RadIntId::U16, &mut data);
-        data.write_all(&typeid.to_le_bytes())
-            .expect("coudn't write to output file");
-
+        let mut aln_tags = TagSection::new_with_label(TagSectionLabel::AlignmentTags);
+        aln_tags.add_tag_desc(TagDesc {
+            name: "compressed_ori_refid".to_owned(),
+            typeid: RadType::Int(RadIntId::U32),
+        });
+        aln_tags.write(&mut data)?;
+
+        // done with tag descriptions
+        // now write the values associated with the file-level tags
         data.write_all(&bclen.to_le_bytes())
             .expect("coudn't write to output file");
         data.write_all(&umilen.to_le_bytes())
@@ -282,11 +347,15 @@ where
     // let initial_cond : bool = false ;
 
     // allocate data
-    let buf_limit = 10000u32;
+    let buf_limit = 10_000u32;
     data = Cursor::new(Vec::<u8>::with_capacity((buf_limit * 24) as usize));
     data.write_all(&local_nrec.to_le_bytes()).unwrap();
     data.write_all(&local_nrec.to_le_bytes()).unwrap();
 
+    // empiricaly derived factor of size of bam vs rad
+    // encoding for records.
+    let approx_bam_to_rad_factor = 6.258_f64;
+
     // calculate number of records
     // let mut total_number_of_records = 0u64;
     // for r in bam.records(){
@@ -301,8 +370,8 @@ where
         .expect("ProgressStyle template was invalid.")
         .progress_chars("╢▌▌░╟");
 
-    let expected_bar_length = bam_bytes / ((buf_limit as u64) * 24);
-    // let expected_bar_length = 50u64 ;// bam_bytes / ((buf_limit as u64) * 24);
+    let expected_bar_length =
+        bam_bytes / (((buf_limit as f64) * 24_f64) * approx_bam_to_rad_factor).round() as u64;
 
     let pbar_inner = ProgressBar::new(expected_bar_length);
     pbar_inner.set_style(sty);
@@ -314,22 +383,27 @@ where
     let mut bc = 0u64;
     let mut umi = 0u64;
     let mut tid_list = Vec::<u32>::new();
-    let mut first_pass = true;
     //for r in bam.records(){
     loop {
-        if !first_pass {
-            let next_record_exists = bam.read(&mut rec).is_some();
-            if !next_record_exists {
-                break;
-            }
+        let rec_res = record_it.next();
+        if rec_res.is_none() {
+            break;
         }
-        first_pass = false;
+        // the iterator returns a result, so
+        // make sure it's an Ok variant here.
+        let rec = match rec_res.unwrap() {
+            Ok(x) => x,
+            Err(e) => bail!("{}", e),
+        };
 
-        // let rec = r.unwrap();
-        let is_reverse = rec.is_reverse();
-        let qname_str = str::from_utf8(rec.qname()).unwrap().to_owned();
+        let flags = rec.flags()?;
+
+        let is_reverse = flags.is_reverse_complemented();
+        let qname_str = str::from_utf8(rec.name().expect("valid name").as_bytes())
+            .unwrap()
+            .to_owned();
         let qname = qname_str;
-        let mut tid = rec.tid() as u32;
+        let mut tid = rec.reference_sequence_id(&hdrv).unwrap().unwrap() as u32;
         if qname == old_qname {
             if !is_reverse {
                 tid |= MASK_LOWER_31_U32;
@@ -338,21 +412,12 @@ where
             // local_nrec += 1;
             continue;
         }
+
         // if this is new read and we need to write info
         // for the last read, _unless_ this is the very
         // first read, in which case we shall continue
         if !tid_list.is_empty() {
-            assert!(!tid_list.is_empty(), "Trying to write empty tid_list");
-            let na = tid_list.len();
-            data.write_all(&(na as u32).to_le_bytes()).unwrap();
-            //bc
-            data.write_all(&(bc as u32).to_le_bytes()).unwrap();
-            //umi
-            data.write_all(&(umi as u32).to_le_bytes()).unwrap();
-            //write tid list
-            for t in tid_list.iter() {
-                data.write_all(&t.to_le_bytes()).unwrap();
-            }
+            write_list(&tid_list, &bc_typeid, bc, &umi_typeid, umi, &mut data)?;
         }
 
         // dump if we reach the buf_limit
@@ -375,25 +440,33 @@ where
             data = Cursor::new(Vec::<u8>::with_capacity((buf_limit * 24) as usize));
             data.write_all(&local_nrec.to_le_bytes()).unwrap();
             data.write_all(&local_nrec.to_le_bytes()).unwrap();
-
-            // for debugging
-            // if num_output_chunks > expected_bar_length-1 {
-            //     break;
-            // }
         }
-        // let tname = tid_lookup.get(&(rec.tid() as u32)).unwrap();
-        // let qname_string = str::from_utf8(rec.qname()).unwrap();
 
         // if this is a new read update the old variables
         {
-            let bc_string_in: &str = if let Ok(Aux::String(bcs)) = rec.aux(b"CR") {
-                bcs
+            let flag_data = rec.data();
+            let bc_string_in: &str = if let Some(Ok(bcs)) = flag_data.get(&CR) {
+                match bcs {
+                    SamTagValue::String(bstr) => {
+                        str::from_utf8(<BStr as AsRef<[u8]>>::as_ref(bstr))?
+                    }
+                    _ => {
+                        bail!("cannot convert non-string (Z) tag into umi string.");
+                    }
+                }
             } else {
                 panic!("Input record missing CR tag!")
             };
 
-            let umi_string_in: &str = if let Ok(Aux::String(umis)) = rec.aux(b"UR") {
-                umis
+            let umi_string_in: &str = if let Some(Ok(umis)) = flag_data.get(&UR) {
+                match umis {
+                    SamTagValue::String(bstr) => {
+                        str::from_utf8(<BStr as AsRef<[u8]>>::as_ref(bstr))?
+                    }
+                    _ => {
+                        bail!("cannot convert non-string (Z) tag into umi string.");
+                    }
+                }
             } else {
                 panic!("Input record missing UR tag!")
             };
@@ -419,36 +492,13 @@ where
             tid_list.push(tid);
             local_nrec += 1;
         }
-        // println!("{:?}\t{:?}\t{:?}\t{:?}\t{:?}\t{:?}",
-        //      qname_string,
-        //      tname,
-        //      bc_string,
-        //      umi_string,
-        //      num_output_chunks,
-        //      local_nrec,
-        // );
-        //na TODO: make is independed of 16-10 length criterion
-        // for debugging
-        // if num_output_chunks > expected_bar_length-1 {
-        //     break;
-        // }
     }
 
     if local_nrec > 0 {
         // println!("In the residual writing part");
         // first fill the buffer with the last remaining read
         if !tid_list.is_empty() {
-            assert!(!tid_list.is_empty(), "Trying to write empty tid_list");
-            let na = tid_list.len();
-            data.write_all(&(na as u32).to_le_bytes()).unwrap();
-            //bc
-            data.write_all(&(bc as u32).to_le_bytes()).unwrap();
-            //umi
-            data.write_all(&(umi as u32).to_le_bytes()).unwrap();
-            //write tid list
-            for t in tid_list.iter() {
-                data.write_all(&t.to_le_bytes()).unwrap();
-            }
+            write_list(&tid_list, &bc_typeid, bc, &umi_typeid, umi, &mut data)?;
         }
 
         data.set_position(0);
@@ -456,7 +506,7 @@ where
         let nrec = local_nrec;
         data.write_all(&nbytes.to_le_bytes()).unwrap();
         data.write_all(&nrec.to_le_bytes()).unwrap();
-        // owriter.lock().unwrap().write_all(data.get_ref()).unwrap();
+
         owriter.write_all(data.get_ref()).unwrap();
         num_output_chunks += 1;
     }
@@ -466,20 +516,6 @@ where
     println!();
     info!(log, "{:?} chunks written", num_output_chunks,);
 
-    // owriter.lock().unwrap().flush();
-    // owriter
-    //     .lock()
-    //     .unwrap()
-    //     .get_ref()
-    //     .seek(SeekFrom::Start(
-    //         end_header_pos,
-    //     ))
-    //     .expect("couldn't seek in output file");
-    // owriter
-    //     .lock()
-    //     .unwrap()
-    //     .write_all(&num_output_chunks.to_le_bytes())
-    //     .expect("couldn't write to output file.");
     owriter.flush().expect("File buffer could not be flushed");
     owriter
         .seek(SeekFrom::Start(end_header_pos))
@@ -489,6 +525,7 @@ where
         .expect("couldn't write to output file.");
 
     info!(log, "finished writing to {:?}.", rad_file.as_ref());
+    Ok(())
 }
 
 pub fn view<P>(rad_file: P, print_header: bool, log: &slog::Logger)
@@ -503,32 +540,21 @@ where
 {
     let i_file = File::open(rad_file).unwrap();
     let mut br = BufReader::new(i_file);
-    let hdr = rad_types::RadHeader::from_bytes(&mut br);
-    // info!(
-    //     log,
-    //     "paired : {:?}, ref_count : {}, num_chunks : {}",
-    //     hdr.is_paired != 0,
-    //     hdr.ref_count.to_formatted_string(&Locale::en),
-    //     hdr.num_chunks.to_formatted_string(&Locale::en)
-    // );
-    // file-level
-    let _fl_tags = rad_types::TagSection::from_bytes(&mut br);
-    // info!(log, "read {:?} file-level tags", fl_tags.tags.len());
-    // read-level
-    let rl_tags = rad_types::TagSection::from_bytes(&mut br);
-    // info!(log, "read {:?} read-level tags", rl_tags.tags.len());
+    let prelude = RadPrelude::from_bytes(&mut br)?;
+    let hdr = &prelude.hdr;
+    let rl_tags = &prelude.read_tags;
 
     // right now, we only handle BC and UMI types of U8—U64, so validate that
     const BNAME: &str = "b";
     const UNAME: &str = "u";
 
-    let mut bct: Option<u8> = None;
-    let mut umit: Option<u8> = None;
+    let mut bct: Option<RadType> = None;
+    let mut umit: Option<RadType> = None;
 
     for rt in &rl_tags.tags {
         // if this is one of our tags
         if rt.name == BNAME || rt.name == UNAME {
-            if rad_types::decode_int_type_tag(rt.typeid).is_none() {
+            if !rt.typeid.is_int_type() {
                 crit!(
                     log,
                     "currently only RAD types 1--4 are supported for 'b' and 'u' tags."
@@ -544,20 +570,22 @@ where
             }
         }
     }
+    assert!(bct.is_some(), "barcode type tag was missing!");
+    assert!(umit.is_some(), "umi type tag was missing!");
 
-    // alignment-level
-    let _al_tags = rad_types::TagSection::from_bytes(&mut br);
-    // info!(log, "read {:?} alignemnt-level tags", al_tags.tags.len());
+    let file_tag_map = prelude.file_tags.parse_tags_from_bytes(&mut br)?;
+    info!(log, "File-level tag map {:?}", file_tag_map);
 
-    let ft_vals = rad_types::FileTags::from_bytes(&mut br);
-    // info!(log, "File-level tag values {:?}", ft_vals);
+    let barcode_tag = file_tag_map
+        .get("cblen")
+        .expect("tag map must contain cblen");
+    let barcode_len: u16 = barcode_tag.try_into()?;
 
-    let mut num_reads: u64 = 0;
+    let umi_tag = file_tag_map.get("ulen").expect("tag map must contain ulen");
+    let umi_len: u16 = umi_tag.try_into()?;
 
-    let bc_type = rad_types::decode_int_type_tag(bct.expect("no barcode tag description present."))
-        .context("unknown barcode type id.")?;
-    let umi_type = rad_types::decode_int_type_tag(umit.expect("no umi tag description present"))
-        .context("unknown barcode type id.")?;
+    let mut num_reads: u64 = 0;
+    let record_context = prelude.get_record_context::<AlevinFryRecordContext>()?;
 
     let stdout = stdout(); // get the global stdout entity
     let stdout_l = stdout.lock();
@@ -576,10 +604,10 @@ where
 
     let mut id = 0usize;
     for _ in 0..(hdr.num_chunks as usize) {
-        let c = rad_types::Chunk::from_bytes(&mut br, &bc_type, &umi_type);
+        let c = chunk::Chunk::<AlevinFryReadRecord>::from_bytes(&mut br, &record_context);
         for read in c.reads.iter() {
-            let bc_mer: BitKmer = (read.bc, ft_vals.bclen as u8);
-            let umi_mer: BitKmer = (read.umi, ft_vals.umilen as u8);
+            let bc_mer: BitKmer = (read.bc, barcode_len as u8);
+            let umi_mer: BitKmer = (read.umi, umi_len as u8);
 
             // let umi = str::from_utf8(&umi_).unwrap();
             let num_entries = read.refs.len();
@@ -589,7 +617,7 @@ where
                     handle,
                     "ID:{}\tHI:{}\tNH:{}\tCB:{}\tUMI:{}\tDIR:{:?}\t{}",
                     id,
-                    i,
+                    i + 1,
                     num_entries,
                     unsafe { std::str::from_utf8_unchecked(&bitmer_to_bytes(bc_mer)[..]) },
                     unsafe { std::str::from_utf8_unchecked(&bitmer_to_bytes(umi_mer)[..]) },
@@ -605,10 +633,6 @@ where
                         return Ok(num_reads);
                     }
                 };
-
-                // writeln!(handle,"{:?}\t{:?}\t{:?}\t{:?}",
-                // bc,umi,read.dirs[i],
-                // str::from_utf8(&tid_),);
             }
             id += 1;
         }
diff --git a/src/em.rs b/src/em.rs
index 35c239d..526dc48 100644
--- a/src/em.rs
+++ b/src/em.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
diff --git a/src/eq_class.rs b/src/eq_class.rs
index aebaf64..1438277 100644
--- a/src/eq_class.rs
+++ b/src/eq_class.rs
@@ -1,8 +1,17 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
 use std::collections::HashMap;
 use std::hash::{BuildHasher, Hasher};
 use std::io::BufRead;
 
-use libradicl::rad_types;
+use libradicl::chunk;
+use libradicl::record::AlevinFryReadRecord;
 
 /**
 * Single-cell equivalence class
@@ -276,7 +285,7 @@ impl EqMap {
     }
 
     #[allow(dead_code)]
-    fn init_from_small_chunk(&mut self, cell_chunk: &mut rad_types::Chunk) {
+    fn init_from_small_chunk(&mut self, cell_chunk: &mut chunk::Chunk<AlevinFryReadRecord>) {
         //let rand_state = ahash::RandomState::with_seeds(2u64, 7u64, 1u64, 8u64);
         let mut hasher = self.eqid_map.hasher().build_hasher();
         //let mut hasher = rand_state.build_hasher();
@@ -345,7 +354,7 @@ impl EqMap {
 
     pub fn init_from_chunk_gene_level(
         &mut self,
-        cell_chunk: &mut rad_types::Chunk,
+        cell_chunk: &mut chunk::Chunk<AlevinFryReadRecord>,
         tid_to_gid: &[u32],
     ) {
         self.eqid_map.clear();
@@ -435,7 +444,7 @@ impl EqMap {
         }
     }
 
-    pub fn init_from_chunk(&mut self, cell_chunk: &mut rad_types::Chunk) {
+    pub fn init_from_chunk(&mut self, cell_chunk: &mut chunk::Chunk<AlevinFryReadRecord>) {
         /*
         if cell_chunk.reads.len() < 10 {
         self.init_from_small_chunk(cell_chunk);
diff --git a/src/infer.rs b/src/infer.rs
index abd70ec..37a7174 100644
--- a/src/infer.rs
+++ b/src/infer.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
diff --git a/src/io_utils.rs b/src/io_utils.rs
index ac92042..5c6a1a3 100644
--- a/src/io_utils.rs
+++ b/src/io_utils.rs
@@ -1,10 +1,21 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * 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;
 use scroll::Pwrite;
 
-use libradicl::rad_types;
+use libradicl::chunk;
+use libradicl::record::{AlevinFryReadRecord, AlevinFryRecordContext};
+
 use std::collections::HashSet;
 use std::io::Read;
 use std::sync::Arc;
@@ -69,7 +80,7 @@ pub(crate) fn fill_work_queue<T: Read>(
         // and we are just filling up the buffer with the last cell, and there will be no more
         // headers left to read, so skip this
         if chunk_num < num_chunks {
-            let (nc, nr) = rad_types::Chunk::read_header(&mut br);
+            let (nc, nr) = chunk::Chunk::<AlevinFryReadRecord>::read_header(&mut br);
             nbytes_chunk = nc;
             nrec_chunk = nr;
         }
@@ -109,18 +120,13 @@ pub(crate) fn fill_work_queue<T: Read>(
 /// any cell whose barcode is not in `keep_set`.
 pub(crate) fn fill_work_queue_filtered<T: Read>(
     keep_set: HashSet<u64, ahash::RandomState>,
-    rl_tags: &rad_types::TagSection,
+    record_context: &AlevinFryRecordContext,
     q: Arc<ArrayQueue<MetaChunk>>,
     mut br: T,
     num_chunks: usize,
     pbar: &ProgressBar,
 ) -> anyhow::Result<()> {
-    let bct = rl_tags.tags[0].typeid;
-    let umit = rl_tags.tags[1].typeid;
-    let bc_type = rad_types::decode_int_type_tag(bct).context("unsupported barcode type id.")?;
-    let umi_type = rad_types::decode_int_type_tag(umit).context("unsupported umi type id.")?;
-
-    const BUFSIZE: usize = 524208;
+    const BUFSIZE: usize = 524_208;
     // the buffer that will hold our records
     let mut buf = vec![0u8; BUFSIZE];
     // the number of bytes currently packed into the chunk
@@ -164,8 +170,10 @@ pub(crate) fn fill_work_queue_filtered<T: Read>(
             br.read_exact(&mut buf[(boffset + 8)..(boffset + nbytes_chunk as usize)])
                 .context("failed to read from queue.")?;
             // get the barcode for this chunk
-            let (bc, _umi) =
-                rad_types::Chunk::peek_record(&buf[boffset + 8..], &bc_type, &umi_type);
+            let (bc, _umi) = chunk::Chunk::<AlevinFryReadRecord>::peek_record(
+                &buf[boffset + 8..],
+                record_context,
+            );
             if keep_set.contains(&bc) {
                 cells_in_chunk += 1;
                 cbytes += nbytes_chunk;
@@ -181,7 +189,7 @@ pub(crate) fn fill_work_queue_filtered<T: Read>(
         // and we are just filling up the buffer with the last cell, and there will be no more
         // headers left to read, so skip this
         if chunk_num < num_chunks {
-            let (nc, nr) = rad_types::Chunk::read_header(&mut br);
+            let (nc, nr) = chunk::Chunk::<AlevinFryReadRecord>::read_header(&mut br);
             nbytes_chunk = nc;
             nrec_chunk = nr;
         }
diff --git a/src/lib.rs b/src/lib.rs
index 2d07e1b..aab2b10 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
diff --git a/src/main.rs b/src/main.rs
index 33fd704..12fd613 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
@@ -344,7 +344,7 @@ fn main() -> anyhow::Result<()> {
             .build();
 
         match generate_permit_list(gpl_opts) {
-            Ok(nc) if nc == 0 => {
+            Ok(0) => {
                 warn!(log, "found 0 corrected barcodes; please check the input.");
             }
             Err(e) => return Err(e),
@@ -358,7 +358,7 @@ fn main() -> anyhow::Result<()> {
         let input_file: &PathBuf = t.get_one("bam").unwrap();
         let rad_file: &PathBuf = t.get_one("output").unwrap();
         let num_threads: u32 = *t.get_one("threads").unwrap();
-        alevin_fry::convert::bam2rad(input_file, rad_file, num_threads, &log)
+        alevin_fry::convert::bam2rad(input_file, rad_file, num_threads, &log)?
     }
 
     // convert a rad file to a textual representation and write to stdout
diff --git a/src/prog_opts.rs b/src/prog_opts.rs
index 760effa..a57a857 100644
--- a/src/prog_opts.rs
+++ b/src/prog_opts.rs
@@ -1,3 +1,12 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
+
 //use derive_builder::Builder;
 use bio_types::strand::Strand;
 use serde::Serialize;
diff --git a/src/pugutils.rs b/src/pugutils.rs
index 2007ba1..f9880af 100644
--- a/src/pugutils.rs
+++ b/src/pugutils.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
@@ -20,7 +20,8 @@ use petgraph::prelude::*;
 use petgraph::unionfind::*;
 use petgraph::visit::NodeIndexable;
 
-use libradicl::rad_types;
+use libradicl::chunk;
+use libradicl::record::AlevinFryReadRecord;
 
 use slog::{crit, info, warn};
 
@@ -294,7 +295,7 @@ where
 
     let mut components = get_map();
     for (i, v) in labels.iter().enumerate() {
-        let ve = components.entry(*v as u32).or_insert_with(Vec::new);
+        let ve = components.entry(*v as u32).or_default();
         ve.push(i as u32);
     }
     components
@@ -626,7 +627,7 @@ fn resolve_num_molecules_crlike_from_vec(
 }
 
 pub fn get_num_molecules_cell_ranger_like_small(
-    cell_chunk: &mut rad_types::Chunk,
+    cell_chunk: &mut chunk::Chunk<AlevinFryReadRecord>,
     tid_to_gid: &[u32],
     _num_genes: usize,
     gene_eqclass_hash: &mut HashMap<Vec<u32>, u32, ahash::RandomState>,
@@ -815,7 +816,7 @@ fn get_num_molecules_large_component(
         let vert = g.from_index(*vertex_id as usize);
         // add the corresponding (UMI, frequency) pair to the map
         // for this eq_id
-        let umis = tmp_map.entry(vert.0).or_insert_with(Vec::new);
+        let umis = tmp_map.entry(vert.0).or_default();
         umis.push(eq_map.eqc_info[vert.0 as usize].umis[vert.1 as usize]);
     }
 
diff --git a/src/quant.rs b/src/quant.rs
index 835dd4f..3d2222f 100644
--- a/src/quant.rs
+++ b/src/quant.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
@@ -43,7 +43,12 @@ use crate::io_utils;
 use crate::prog_opts::QuantOpts;
 use crate::pugutils;
 use crate::utils as afutils;
-use libradicl::rad_types;
+
+use libradicl::{
+    chunk,
+    header::RadPrelude,
+    record::{AlevinFryReadRecord, AlevinFryRecordContext},
+};
 
 type BufferedGzFile = BufWriter<GzEncoder<fs::File>>;
 
@@ -344,7 +349,10 @@ pub fn quantify(quant_opts: QuantOpts) -> anyhow::Result<()> {
 // with these options
 pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<()> {
     let parent = std::path::Path::new(quant_opts.input_dir);
-    let hdr = rad_types::RadHeader::from_bytes(&mut br);
+
+    let prelude = RadPrelude::from_bytes(&mut br)?;
+    let hdr = &prelude.hdr;
+    //let hdr = rad_types::RadHeader::from_bytes(&mut br);
 
     let init_uniform = quant_opts.init_uniform;
     let summary_stat = quant_opts.summary_stat;
@@ -461,25 +469,29 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
         Arc::new(bincode::deserialize_from(&bc_unmapped_file).unwrap());
 
     // file-level
-    let fl_tags = rad_types::TagSection::from_bytes(&mut br);
+    let fl_tags = &prelude.file_tags;
     info!(log, "read {:?} file-level tags", fl_tags.tags.len());
     // read-level
-    let rl_tags = rad_types::TagSection::from_bytes(&mut br);
+    let rl_tags = &prelude.read_tags;
     info!(log, "read {:?} read-level tags", rl_tags.tags.len());
     // alignment-level
-    let al_tags = rad_types::TagSection::from_bytes(&mut br);
+    let al_tags = &prelude.aln_tags;
     info!(log, "read {:?} alignemnt-level tags", al_tags.tags.len());
 
-    let ft_vals = rad_types::FileTags::from_bytes(&mut br);
-    info!(log, "File-level tag values {:?}", ft_vals);
+    let file_tag_map = prelude.file_tags.parse_tags_from_bytes(&mut br)?;
+    info!(log, "File-level tag values {:?}", file_tag_map);
 
-    let bct = rl_tags.tags[0].typeid;
-    let umit = rl_tags.tags[1].typeid;
+    let barcode_tag = file_tag_map
+        .get("cblen")
+        .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 {
-        match afutils::read_filter_list(fname, ft_vals.bclen) {
+        match afutils::read_filter_list(fname, barcode_len) {
             Ok(fset) => {
                 // the number of cells we expect to
                 // actually process
@@ -534,9 +546,12 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
     let tid_to_gid_shared = std::sync::Arc::new(tid_to_gid);
     // the number of reference sequences
     let ref_count = hdr.ref_count as u32;
+
+    // TODO -- maybe delete March 5, 2024
     // the types for the barcodes and umis
-    let bc_type = rad_types::decode_int_type_tag(bct).expect("unsupported barcode type id.");
-    let umi_type = rad_types::decode_int_type_tag(umit).expect("unsupported umi type id.");
+    // let bc_type = rad_types::decode_int_type_tag(bct).expect("unsupported barcode type id.");
+    // let umi_type = rad_types::decode_int_type_tag(umit).expect("unsupported umi type id.");
+
     // the number of genes (different than the number of reference sequences, which are transcripts)
     let num_genes = gene_name_to_id.len();
 
@@ -636,15 +651,19 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
         let tid_to_gid = tid_to_gid_shared.clone();
         // 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;
+        // let bc_type = bc_type;
+        // let umi_type = umi_type;
+
         // and the file writer
         let bcout = bc_writer.clone();
         // global gene-level eqc map
         let eqid_map_lockc = eqid_map_lock.clone();
         // and will need to know the barcode length
-        let bclen = ft_vals.bclen;
+        let bclen = barcode_len;
         let alt_res_cells = alt_res_cells.clone();
         let empty_resolved_cells = empty_resolved_cells.clone();
         let unmapped_count = bc_unmapped_map.clone();
@@ -738,7 +757,10 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
                             BufReader::new(&buf[byte_offset..(byte_offset + nbytes as usize)]);
                         byte_offset += nbytes as usize;
 
-                        let mut c = rad_types::Chunk::from_bytes(&mut nbr, &bc_type, &umi_type);
+                        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);
                         }
@@ -1198,7 +1220,7 @@ pub fn do_quantify<T: Read>(mut br: T, quant_opts: QuantOpts) -> anyhow::Result<
         // we have a retained set
         io_utils::fill_work_queue_filtered(
             ret_bc,
-            &rl_tags,
+            &record_context,
             q,
             br,
             hdr.num_chunks as usize,
diff --git a/src/utils.rs b/src/utils.rs
index 0b42881..0e54c74 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -1,3 +1,11 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
 use crate::constants as afconst;
 use crate::eq_class::IndexedEqList;
 use anyhow::{anyhow, Context};
@@ -561,8 +569,7 @@ pub fn get_all_snps(bc: u64, bc_length: usize) -> Vec<u64> {
         "barcode length greater than 32 not supported"
     );
 
-    let mut snps: Vec<u64> = Vec::new();
-    snps.reserve(3 * bc_length);
+    let mut snps: Vec<u64> = Vec::with_capacity(3 * bc_length);
 
     for nt_index in 1..=bc_length {
         // clearing the two relevant bits based on nucleotide position
@@ -590,8 +597,7 @@ pub fn get_all_indels(bc: u64, bc_length: usize) -> Vec<u64> {
         "barcode length greater than 32 not supported"
     );
 
-    let mut indels: Vec<u64> = Vec::new();
-    indels.reserve(8 * (bc_length - 1));
+    let mut indels: Vec<u64> = Vec::with_capacity(8 * (bc_length - 1));
 
     for nt_index in 1..bc_length {
         let mut bit_mask = 1 << (2 * nt_index);