From cbd86bd3f2a34d9b68d8558d0d129ffedb8c65cf Mon Sep 17 00:00:00 2001
From: Rob Patro <rob@newton>
Date: Fri, 12 Jul 2024 12:33:36 -0400
Subject: [PATCH] upgrade some deps, depend on alevin-fry >= 0.10.0 in env file

---
 ...ease-please.yml => release-please.yml.bak} |   0
 Cargo.lock                                    | 496 +++++++++---------
 Cargo.toml                                    |   8 +-
 simpleaf_conda_env.yml                        |   2 +-
 4 files changed, 250 insertions(+), 256 deletions(-)
 rename .github/workflows/{release-please.yml => release-please.yml.bak} (100%)

diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml.bak
similarity index 100%
rename from .github/workflows/release-please.yml
rename to .github/workflows/release-please.yml.bak
diff --git a/Cargo.lock b/Cargo.lock
index c0dd138..10cb785 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -10,9 +10,9 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
 
 [[package]]
 name = "ahash"
-version = "0.8.7"
+version = "0.8.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77c3a9648d43b9cd48db467b3f87fdd6e146bcc88ab0180006cef2179fe11d01"
+checksum = "e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011"
 dependencies = [
  "cfg-if",
  "getrandom",
@@ -32,9 +32,9 @@ dependencies = [
 
 [[package]]
 name = "allocator-api2"
-version = "0.2.16"
+version = "0.2.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5"
+checksum = "5c6cb57a04249c6480766f7f7cef5467412af1490f8d1e243141daddada3264f"
 
 [[package]]
 name = "android-tzdata"
@@ -93,18 +93,18 @@ dependencies = [
 
 [[package]]
 name = "anstyle-query"
-version = "1.0.3"
+version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a64c907d4e79225ac72e2a354c9ce84d50ebb4586dee56c82b3ee73004f537f5"
+checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391"
 dependencies = [
  "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.2"
+version = "3.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7"
+checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19"
 dependencies = [
  "anstyle",
  "windows-sys 0.52.0",
@@ -112,15 +112,15 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.79"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "080e9890a082662b09c1ad45f567faeeb47f22b5fb23895fbe1e651e718e25ca"
+checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da"
 
 [[package]]
 name = "argminmax"
-version = "0.6.1"
+version = "0.6.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "202108b46429b765ef483f8a24d5c46f48c14acfdacc086dd4ab6dddf6bcdbd2"
+checksum = "52424b59d69d69d5056d508b260553afd91c57e21849579cd1f50ee8b8b88eaa"
 dependencies = [
  "num-traits",
 ]
@@ -203,44 +203,43 @@ dependencies = [
 
 [[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 = "3.14.0"
+version = "3.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec"
+checksum = "79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c"
 
 [[package]]
 name = "bytecount"
-version = "0.6.7"
+version = "0.6.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205"
+checksum = "5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce"
 
 [[package]]
 name = "bytemuck"
-version = "1.14.1"
+version = "1.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ed2490600f404f2b94c167e31d3ed1d5f3c225a0f3b80230053b3e0b7b962bd9"
+checksum = "b236fc92302c97ed75b38da1f4917b5cdda4984745740f153a5d3059e48d725e"
 dependencies = [
  "bytemuck_derive",
 ]
 
 [[package]]
 name = "bytemuck_derive"
-version = "1.5.0"
+version = "1.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "965ab7eb5f8f97d2a083c799f3a1b994fc397b2fe2da5d1da1626ce15a39f2b1"
+checksum = "1ee891b04274a59bd38b412188e24b849617b2e45a0fd8d057deb63e7403761b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -251,9 +250,9 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bytes"
-version = "1.5.0"
+version = "1.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223"
+checksum = "514de17de45fdb8dc022b1a7975556c53c86f9f0aa5f534b98977b171857c2c9"
 
 [[package]]
 name = "bzip2"
@@ -278,9 +277,9 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.0.98"
+version = "1.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "41c270e7540d725e65ac7f1b212ac8ce349719624d7bcff99f8e2e488e8cf03f"
+checksum = "907d8581360765417f8f2e0e7d602733bbed60156b4465b7617243689ef9b83d"
 dependencies = [
  "jobserver",
  "libc",
@@ -304,14 +303,14 @@ dependencies = [
  "js-sys",
  "num-traits",
  "wasm-bindgen",
- "windows-targets 0.52.4",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
 name = "clap"
-version = "4.5.8"
+version = "4.5.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "84b3edb18336f4df585bc9aa31dd99c036dfa5dc5e9a2939a722a188f3a8970d"
+checksum = "64acc1846d54c1fe936a78dc189c34e28d3f5afc348403f28ecf53660b9b8462"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -319,9 +318,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.5.8"
+version = "4.5.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c1c09dd5ada6c6c78075d6fd0da3f90d8080651e2d6cc8eb2f1aaa4034ced708"
+checksum = "6fb8393d67ba2e7bfaf28a23458e4e2b543cc73a99595511eb207fdb8aede942"
 dependencies = [
  "anstream",
  "anstyle",
@@ -339,7 +338,7 @@ dependencies = [
  "heck 0.5.0",
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -382,13 +381,13 @@ checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422"
 
 [[package]]
 name = "comfy-table"
-version = "7.1.0"
+version = "7.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7c64043d6c7b7a4c58e39e7efccfdea7b93d885a795d0c054a69dbbf4dd52686"
+checksum = "b34115915337defe99b2aff5c2ce6771e5fbc4079f4b506301f5cf394c8452f7"
 dependencies = [
  "crossterm",
- "strum 0.25.0",
- "strum_macros 0.25.3",
+ "strum",
+ "strum_macros 0.26.4",
  "unicode-width",
 ]
 
@@ -409,18 +408,18 @@ dependencies = [
 
 [[package]]
 name = "crc32fast"
-version = "1.3.2"
+version = "1.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d"
+checksum = "a97769d94ddab943e4510d138150169a2758b5ef3eb191a9ee688de3e23ef7b3"
 dependencies = [
  "cfg-if",
 ]
 
 [[package]]
 name = "crossbeam-channel"
-version = "0.5.11"
+version = "0.5.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "176dc175b78f56c0f321911d9c8eb2b77a78a4860b9c19db83835fea1a46649b"
+checksum = "33480d6946193aa8033910124896ca395333cae7e2d1113d1fef6c3272217df2"
 dependencies = [
  "crossbeam-utils",
 ]
@@ -455,9 +454,9 @@ dependencies = [
 
 [[package]]
 name = "crossbeam-utils"
-version = "0.8.19"
+version = "0.8.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345"
+checksum = "22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80"
 
 [[package]]
 name = "crossterm"
@@ -545,26 +544,26 @@ dependencies = [
 
 [[package]]
 name = "dyn-clone"
-version = "1.0.16"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "545b22097d44f8a9581187cdf93de7a71e4722bf51200cfaba810865b49a495d"
+checksum = "0d6ef0072f8a535281e4876be788938b528e9a1d43900b82c2569af7da799125"
 
 [[package]]
 name = "either"
-version = "1.12.0"
+version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3dca9240753cf90908d7e4aac30f630662b02aebaa1b58a3cadabdb23385b58b"
+checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0"
 
 [[package]]
 name = "enum_dispatch"
-version = "0.3.12"
+version = "0.3.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8f33313078bb8d4d05a2733a94ac4c2d8a0df9a2b84424ebf4f33bfc224a890e"
+checksum = "aa18ce2bc66555b3218614519ac839ddb759a7d6720732f979ef8d13be147ecd"
 dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -621,15 +620,15 @@ checksum = "95765f67b4b18863968b4a1bd5bb576f732b29a4a28c7cd84c09fa3e2875f33c"
 
 [[package]]
 name = "fastrand"
-version = "2.0.1"
+version = "2.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "25cbce373ec4653f1a01a31e8a5e5ec0c622dc27ff9c4e6606eefef5cbbed4a5"
+checksum = "9fc0510504f03c51ada170672ac806f1f105a88aa97a5281117e1ddc3368e51a"
 
 [[package]]
 name = "flate2"
-version = "1.0.28"
+version = "1.0.30"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e"
+checksum = "5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae"
 dependencies = [
  "crc32fast",
  "libz-sys",
@@ -695,7 +694,7 @@ checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
 [[package]]
 name = "grangers"
 version = "0.4.0"
-source = "git+https://github.com/COMBINE-lab/grangers.git?branch=dev#eb66072cc70ef95dfd53d48943e63c5e0fa446ba"
+source = "git+https://github.com/COMBINE-lab/grangers.git?branch=main#1b0b0785156e659e261b40153c77f5a21593fa5b"
 dependencies = [
  "anyhow",
  "clap",
@@ -727,9 +726,9 @@ dependencies = [
 
 [[package]]
 name = "hashbrown"
-version = "0.14.3"
+version = "0.14.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604"
+checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
 dependencies = [
  "ahash",
  "allocator-api2",
@@ -750,9 +749,9 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
 [[package]]
 name = "hermit-abi"
-version = "0.3.4"
+version = "0.3.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d3d0e0f38255e7fa3cf31335b3a56f05febd18025f4db5ef7a0cfb4f8da651f"
+checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024"
 
 [[package]]
 name = "home"
@@ -804,12 +803,12 @@ dependencies = [
 
 [[package]]
 name = "indexmap"
-version = "2.2.1"
+version = "2.2.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "433de089bd45971eecf4668ee0ee8f4cec17db4f8bd8f7bc3197a6ce37aa7d9b"
+checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26"
 dependencies = [
  "equivalent",
- "hashbrown 0.14.3",
+ "hashbrown 0.14.5",
 ]
 
 [[package]]
@@ -890,9 +889,9 @@ dependencies = [
 
 [[package]]
 name = "jrsonnet-gcmodule"
-version = "0.3.6"
+version = "0.3.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c11fb98940a7f8b419619e98ccbf2e094671a5fdd0e277f05acd373071186d57"
+checksum = "47975473b24b4503acee0d449fd5eda04ae18828f9811828a6cc99abbbbc38c8"
 dependencies = [
  "jrsonnet-gcmodule-derive",
  "parking_lot",
@@ -900,13 +899,13 @@ dependencies = [
 
 [[package]]
 name = "jrsonnet-gcmodule-derive"
-version = "0.3.6"
+version = "0.3.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6bee774b7ba86fc86ee84482cd6732aa860ae3559f9827c65efd75c51e66ac76"
+checksum = "4782d1d76731f5e5bb4bdeff26ed3350f21d662f178ce6dee7b4da810e7a8f72"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 1.0.109",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -978,9 +977,9 @@ dependencies = [
 
 [[package]]
 name = "js-sys"
-version = "0.3.67"
+version = "0.3.69"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9a1d36f1235bc969acba30b7f5990b864423a6068a10f7c90ae8f0112e3a59d1"
+checksum = "29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d"
 dependencies = [
  "wasm-bindgen",
 ]
@@ -996,9 +995,9 @@ dependencies = [
 
 [[package]]
 name = "lazy_static"
-version = "1.4.0"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
 name = "lexical"
@@ -1087,9 +1086,9 @@ checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
 [[package]]
 name = "libz-sys"
-version = "1.1.15"
+version = "1.1.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "037731f5d3aaa87a5675e895b63ddff1a87624bc29f77004ea829809654e48f6"
+checksum = "c15da26e5af7e25c90b37a2d75cdbf940cf4a55316de9d84c679c9b8bfabf82e"
 dependencies = [
  "cc",
  "pkg-config",
@@ -1104,15 +1103,15 @@ checksum = "0717cef1bc8b636c6e1c1bbdefc09e6322da8a9321966e8928ef80d20f7f770f"
 
 [[package]]
 name = "linux-raw-sys"
-version = "0.4.13"
+version = "0.4.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "01cda141df6706de531b6c46c3a33ecca755538219bd484262fa09410c13539c"
+checksum = "78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89"
 
 [[package]]
 name = "lock_api"
-version = "0.4.11"
+version = "0.4.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
+checksum = "07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17"
 dependencies = [
  "autocfg",
  "scopeguard",
@@ -1120,15 +1119,15 @@ dependencies = [
 
 [[package]]
 name = "log"
-version = "0.4.21"
+version = "0.4.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
+checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
 
 [[package]]
 name = "lz4"
-version = "1.24.0"
+version = "1.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7e9e2dd86df36ce760a60f6ff6ad526f7ba1f14ba0356f8254fb6905e6494df1"
+checksum = "d6eab492fe7f8651add23237ea56dbf11b3c4ff762ab83d40a47f11433421f91"
 dependencies = [
  "libc",
  "lz4-sys",
@@ -1136,9 +1135,9 @@ dependencies = [
 
 [[package]]
 name = "lz4-sys"
-version = "1.9.4"
+version = "1.9.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "57d27b317e207b10f69f5e75494119e391a96f48861ae870d1da6edac98ca900"
+checksum = "e9764018d143cc854c9f17f0b907de70f14393b1f502da6375dce70f00514eb3"
 dependencies = [
  "cc",
  "libc",
@@ -1172,9 +1171,9 @@ checksum = "490cc448043f947bae3cbee9c203358d62dbee0db12107a74be5c30ccfd09771"
 
 [[package]]
 name = "memchr"
-version = "2.7.2"
+version = "2.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
+checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "memmap2"
@@ -1196,9 +1195,9 @@ dependencies = [
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.1"
+version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7"
+checksum = "b8a240ddb74feaf34a79a7add65a741f3167852fba007066dcac1ca548d89c08"
 dependencies = [
  "adler",
 ]
@@ -1220,9 +1219,9 @@ dependencies = [
 
 [[package]]
 name = "multiversion"
-version = "0.7.3"
+version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b2c7b9d7fe61760ce5ea19532ead98541f6b4c495d87247aff9826445cf6872a"
+checksum = "c4851161a11d3ad0bf9402d90ffc3967bf231768bfd7aeb61755ad06dbf1a142"
 dependencies = [
  "multiversion-macros",
  "target-features",
@@ -1230,9 +1229,9 @@ dependencies = [
 
 [[package]]
 name = "multiversion-macros"
-version = "0.7.3"
+version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26a83d8500ed06d68877e9de1dde76c1dbb83885dcdbda4ef44ccbc3fbda2ac8"
+checksum = "79a74ddee9e0c27d2578323c13905793e91622148f138ba29738f9dddb835e90"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1305,7 +1304,7 @@ checksum = "e0531175d5473e6057c1724c1242b19bfc42dba644fe275b4df89c5b8d31a782"
 dependencies = [
  "bit-vec",
  "byteorder",
- "indexmap 2.2.1",
+ "indexmap 2.2.6",
  "noodles-bgzf",
  "noodles-core",
 ]
@@ -1328,7 +1327,7 @@ version = "0.23.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2a70052d45f0bf58198617f282a6564c2c22602aa9bfff293a30b90060148ce6"
 dependencies = [
- "indexmap 2.2.1",
+ "indexmap 2.2.6",
  "noodles-bgzf",
  "noodles-core",
  "noodles-csi",
@@ -1429,9 +1428,9 @@ dependencies = [
 
 [[package]]
 name = "os_pipe"
-version = "1.1.5"
+version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "57119c3b893986491ec9aa85056780d3a0f3cf4da7cc09dd3650dbd6c6738fb9"
+checksum = "29d73ba8daf8fac13b0501d1abeddcfe21ba7401ada61a819144b6c2a4f32209"
 dependencies = [
  "libc",
  "windows-sys 0.52.0",
@@ -1456,9 +1455,9 @@ dependencies = [
 
 [[package]]
 name = "parking_lot"
-version = "0.12.1"
+version = "0.12.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f"
+checksum = "f1bf18183cf54e8d6059647fc3063646a1801cf30896933ec2311622cc4b9a27"
 dependencies = [
  "lock_api",
  "parking_lot_core",
@@ -1466,15 +1465,15 @@ dependencies = [
 
 [[package]]
 name = "parking_lot_core"
-version = "0.9.9"
+version = "0.9.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e"
+checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
 dependencies = [
  "cfg-if",
  "libc",
  "redox_syscall",
  "smallvec",
- "windows-targets 0.48.5",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -1485,15 +1484,15 @@ checksum = "8835116a5c179084a830efb3adc117ab007512b535bc1a21c991d3b32a6b44dd"
 
 [[package]]
 name = "peak_alloc"
-version = "0.2.0"
+version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "84d3978b0aa7d46c34452384c28264ac859c652b67635f6acfd598e1b6608de5"
+checksum = "29c4e8e2dd832fd76346468f822e4e600d30ba4e5aa545a128abf12cfae7ea3e"
 
 [[package]]
 name = "peg"
-version = "0.8.2"
+version = "0.8.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "400bcab7d219c38abf8bd7cc2054eb9bbbd4312d66f6a5557d572a203f646f61"
+checksum = "8a625d12ad770914cbf7eff6f9314c3ef803bfe364a1b20bc36ddf56673e71e5"
 dependencies = [
  "peg-macros",
  "peg-runtime",
@@ -1501,9 +1500,9 @@ dependencies = [
 
 [[package]]
 name = "peg-macros"
-version = "0.8.2"
+version = "0.8.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46e61cce859b76d19090f62da50a9fe92bab7c2a5f09e183763559a2ac392c90"
+checksum = "f241d42067ed3ab6a4fece1db720838e1418f36d868585a27931f95d6bc03582"
 dependencies = [
  "peg-runtime",
  "proc-macro2",
@@ -1512,9 +1511,9 @@ dependencies = [
 
 [[package]]
 name = "peg-runtime"
-version = "0.8.2"
+version = "0.8.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "36bae92c60fa2398ce4678b98b2c4b5a7c61099961ca1fa305aec04a9ad28922"
+checksum = "e3aeb8f54c078314c2065ee649a7241f46b9d8e418e1a9581ba0546657d7aa3a"
 
 [[package]]
 name = "percent-encoding"
@@ -1524,9 +1523,9 @@ checksum = "e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e"
 
 [[package]]
 name = "pest"
-version = "2.7.6"
+version = "2.7.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1f200d8d83c44a45b21764d1916299752ca035d15ecd46faca3e9a2a2bf6ad06"
+checksum = "cd53dff83f26735fdc1ca837098ccf133605d794cdae66acfc2bfac3ec809d95"
 dependencies = [
  "memchr",
  "thiserror",
@@ -1535,9 +1534,9 @@ dependencies = [
 
 [[package]]
 name = "pest_derive"
-version = "2.7.6"
+version = "2.7.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bcd6ab1236bbdb3a49027e920e693192ebfe8913f6d60e294de57463a493cfde"
+checksum = "2a548d2beca6773b1c244554d36fcf8548a8a58e74156968211567250e48e49a"
 dependencies = [
  "pest",
  "pest_generator",
@@ -1545,22 +1544,22 @@ dependencies = [
 
 [[package]]
 name = "pest_generator"
-version = "2.7.6"
+version = "2.7.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2a31940305ffc96863a735bef7c7994a00b325a7138fdbc5bda0f1a0476d3275"
+checksum = "3c93a82e8d145725dcbaf44e5ea887c8a869efdcc28706df2d08c69e17077183"
 dependencies = [
  "pest",
  "pest_meta",
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
 name = "pest_meta"
-version = "2.7.6"
+version = "2.7.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a7ff62f5259e53b78d1af898941cdcdccfae7385cf7d793a6e55de5d05bb4b7d"
+checksum = "a941429fea7e08bedec25e4f6785b6ffaacc6b755da98df5ef3e7dcf4a124c4f"
 dependencies = [
  "once_cell",
  "pest",
@@ -1632,7 +1631,7 @@ dependencies = [
  "phf_shared 0.11.2",
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -1655,9 +1654,9 @@ dependencies = [
 
 [[package]]
 name = "pin-project-lite"
-version = "0.2.13"
+version = "0.2.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8afb450f006bf6385ca15ef45d71d2288452bc3683ce2e2cacc0d18e4be60b58"
+checksum = "bda66fc9667c18cb2758a2ac84d1167245054bcf85d5d1aaa6923f45801bdd02"
 
 [[package]]
 name = "pin-utils"
@@ -1667,9 +1666,9 @@ checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184"
 
 [[package]]
 name = "pkg-config"
-version = "0.3.29"
+version = "0.3.30"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2900ede94e305130c13ddd391e0ab7cbaeb783945ae07a279c268cb05109c6cb"
+checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec"
 
 [[package]]
 name = "planus"
@@ -1711,7 +1710,7 @@ dependencies = [
  "ethnum",
  "foreign_vec",
  "getrandom",
- "hashbrown 0.14.3",
+ "hashbrown 0.14.5",
  "lexical-core",
  "lz4",
  "multiversion",
@@ -1736,8 +1735,8 @@ dependencies = [
  "chrono",
  "comfy-table",
  "either",
- "hashbrown 0.14.3",
- "indexmap 2.2.1",
+ "hashbrown 0.14.5",
+ "indexmap 2.2.6",
  "num-traits",
  "once_cell",
  "polars-arrow",
@@ -1829,8 +1828,8 @@ dependencies = [
  "argminmax",
  "bytemuck",
  "either",
- "hashbrown 0.14.3",
- "indexmap 2.2.1",
+ "hashbrown 0.14.5",
+ "indexmap 2.2.6",
  "memchr",
  "num-traits",
  "polars-arrow",
@@ -1852,7 +1851,7 @@ dependencies = [
  "crossbeam-channel",
  "crossbeam-queue",
  "enum_dispatch",
- "hashbrown 0.14.3",
+ "hashbrown 0.14.5",
  "num-traits",
  "polars-arrow",
  "polars-core",
@@ -1944,7 +1943,7 @@ checksum = "55d2c038ff67e4eb6019682c3f66d83f744e285de9c28e816109a61bace824cd"
 dependencies = [
  "ahash",
  "bytemuck",
- "hashbrown 0.14.3",
+ "hashbrown 0.14.5",
  "num-traits",
  "once_cell",
  "polars-error",
@@ -2062,9 +2061,9 @@ dependencies = [
 
 [[package]]
 name = "rayon"
-version = "1.8.1"
+version = "1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fa7237101a77a10773db45d62004a272517633fbcc3df19d96455ede1122e051"
+checksum = "b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa"
 dependencies = [
  "either",
  "rayon-core",
@@ -2082,23 +2081,23 @@ dependencies = [
 
 [[package]]
 name = "redox_syscall"
-version = "0.4.1"
+version = "0.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
+checksum = "c82cf8cff14456045f55ec4241383baeff27af886adb72ffb2162f99911de0fd"
 dependencies = [
- "bitflags 1.3.2",
+ "bitflags 2.6.0",
 ]
 
 [[package]]
 name = "regex"
-version = "1.10.4"
+version = "1.10.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c"
+checksum = "b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f"
 dependencies = [
  "aho-corasick",
  "memchr",
- "regex-automata 0.4.6",
- "regex-syntax 0.8.3",
+ "regex-automata 0.4.7",
+ "regex-syntax 0.8.4",
 ]
 
 [[package]]
@@ -2112,13 +2111,13 @@ dependencies = [
 
 [[package]]
 name = "regex-automata"
-version = "0.4.6"
+version = "0.4.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea"
+checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df"
 dependencies = [
  "aho-corasick",
  "memchr",
- "regex-syntax 0.8.3",
+ "regex-syntax 0.8.4",
 ]
 
 [[package]]
@@ -2129,28 +2128,29 @@ checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1"
 
 [[package]]
 name = "regex-syntax"
-version = "0.8.3"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56"
+checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b"
 
 [[package]]
 name = "ring"
-version = "0.17.7"
+version = "0.17.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "688c63d65483050968b2a8937f7995f443e27041a0f7700aa59b0822aedebb74"
+checksum = "c17fa4cb658e3583423e915b9f3acc01cceaee1860e33d59ebae66adc3a2dc0d"
 dependencies = [
  "cc",
+ "cfg-if",
  "getrandom",
  "libc",
  "spin",
  "untrusted",
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "roers"
 version = "0.3.0"
-source = "git+https://github.com/COMBINE-lab/roers?branch=main#a1cb54e79c2cb2c0af1d2c9ba92e1e3b3b6f63cd"
+source = "git+https://github.com/COMBINE-lab/roers?branch=main#8ed7edc8d5af4f8b97cc96c20fd8fd5107155f69"
 dependencies = [
  "anyhow",
  "clap",
@@ -2206,9 +2206,9 @@ dependencies = [
 
 [[package]]
 name = "rustls"
-version = "0.21.10"
+version = "0.21.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f9d5a6813c0759e4609cd494e8e725babae6a2ca7b62a5536a13daaec6fcb7ba"
+checksum = "3f56a14d1f48b391359b22f731fd4bd7e43c97f3c50eee276f3aa09c94784d3e"
 dependencies = [
  "log",
  "ring",
@@ -2228,9 +2228,9 @@ dependencies = [
 
 [[package]]
 name = "rustversion"
-version = "1.0.14"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4"
+checksum = "955d28af4278de8121b7ebeb796b6a45735dc01436d898801014aced2773a3d6"
 
 [[package]]
 name = "ryu"
@@ -2238,12 +2238,6 @@ version = "1.0.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
 
-[[package]]
-name = "safemem"
-version = "0.3.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef703b7cb59335eae2eb93ceb664c0eb7ea6bf567079d843e09420219668e072"
-
 [[package]]
 name = "scopeguard"
 version = "1.2.0"
@@ -2295,29 +2289,29 @@ dependencies = [
 
 [[package]]
 name = "serde"
-version = "1.0.203"
+version = "1.0.204"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7253ab4de971e72fb7be983802300c30b5a7f0c2e56fab8abfc6a214307c0094"
+checksum = "bc76f558e0cbb2a839d37354c575f1dc3fdc6546b5be373ba43d95f231bf7c12"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.203"
+version = "1.0.204"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "500cbc0ebeb6f46627f50f3f5811ccf6bf00643be300b4c3eabc0ef55dc5b5ba"
+checksum = "e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
 name = "serde_json"
-version = "1.0.119"
+version = "1.0.120"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e8eddb61f0697cc3989c5d64b452f5488e2b8a60fd7d5076a3045076ffef8cb0"
+checksum = "4e0d21c9a8cae1235ad58a00c11cb40d4b1e5c784f1ef2c537876ed6ffd8b7c5"
 dependencies = [
  "itoa",
  "ryu",
@@ -2385,7 +2379,7 @@ checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a"
 
 [[package]]
 name = "simpleaf"
-version = "0.17.1"
+version = "0.17.2"
 dependencies = [
  "anyhow",
  "chrono",
@@ -2403,7 +2397,7 @@ dependencies = [
  "seq_geom_xform",
  "serde",
  "serde_json",
- "strum 0.26.3",
+ "strum",
  "strum_macros 0.26.4",
  "tabled",
  "thiserror",
@@ -2421,9 +2415,9 @@ checksum = "38b58827f4464d87d377d175e90bf58eb00fd8716ff0a62f80356b5e61555d0d"
 
 [[package]]
 name = "smallvec"
-version = "1.13.1"
+version = "1.13.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7"
+checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
 
 [[package]]
 name = "smartstring"
@@ -2503,12 +2497,6 @@ dependencies = [
  "syn 1.0.109",
 ]
 
-[[package]]
-name = "strum"
-version = "0.25.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "290d54ea6f91c969195bdbcd7442c8c2a2ba87da8bf60a7ee86a235d4bc1e125"
-
 [[package]]
 name = "strum"
 version = "0.26.3"
@@ -2529,7 +2517,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -2542,7 +2530,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -2558,9 +2546,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.68"
+version = "2.0.71"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "901fa70d88b9d6c98022e23b4136f9f3e54e4662c3bc1bd1d84a42a9a0f0c1e9"
+checksum = "b146dcf730474b4bcd16c311627b31ede9ab149045db4d6088b3becaea046462"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -2613,19 +2601,18 @@ checksum = "55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369"
 
 [[package]]
 name = "target-features"
-version = "0.1.5"
+version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cfb5fa503293557c5158bd215fdc225695e567a77e453f5d4452a50a193969bd"
+checksum = "c1bbb9f3c5c463a01705937a24fdabc5047929ac764b2d5b9cf681c1f5041ed5"
 
 [[package]]
 name = "tempfile"
-version = "3.9.0"
+version = "3.10.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "01ce4141aa927a6d1bd34a041795abd0db1cccba5d5f24b009f694bdf3a1f3fa"
+checksum = "85b77fafb263dd9d05cbeac119526425676db3784113aa9295c88498cbf8bff1"
 dependencies = [
  "cfg-if",
  "fastrand",
- "redox_syscall",
  "rustix",
  "windows-sys 0.52.0",
 ]
@@ -2651,22 +2638,22 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.56"
+version = "1.0.62"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d54378c645627613241d077a3a79db965db602882668f9136ac42af9ecb730ad"
+checksum = "f2675633b1499176c2dff06b0856a27976a8f9d436737b4cf4f312d4d91d8bbb"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.56"
+version = "1.0.62"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fa0faa943b50f3db30a20aa7e265dbc66076993efed8463e8de414e5d06d3471"
+checksum = "d20468752b09f49e909e55a5d338caa8bedf615594e9d80bc4c565d30faf798c"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -2677,9 +2664,9 @@ checksum = "3bf63baf9f5039dadc247375c29eb13706706cfde997d0330d05aa63a77d8820"
 
 [[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",
@@ -2735,7 +2722,7 @@ checksum = "34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -2797,9 +2784,9 @@ checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
 
 [[package]]
 name = "unicode-width"
-version = "0.1.11"
+version = "0.1.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e51733f11c9c4f72aa0c160008246859e340b00807569a0da0e7a1079b27ba85"
+checksum = "0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d"
 
 [[package]]
 name = "untrusted"
@@ -2809,9 +2796,9 @@ checksum = "8ecb6da28b8a351d773b68d5825ac39017e680750f980f3a1a85cd8dd28a47c1"
 
 [[package]]
 name = "utf8parse"
-version = "0.2.1"
+version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
+checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
 
 [[package]]
 name = "valuable"
@@ -2839,9 +2826,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.90"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b1223296a201415c7fad14792dbefaace9bd52b62d33453ade1c5b5f07555406"
+checksum = "4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8"
 dependencies = [
  "cfg-if",
  "wasm-bindgen-macro",
@@ -2849,24 +2836,24 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-backend"
-version = "0.2.90"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fcdc935b63408d58a32f8cc9738a0bffd8f05cc7c002086c6ef20b7312ad9dcd"
+checksum = "614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da"
 dependencies = [
  "bumpalo",
  "log",
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.90"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3e4c238561b2d428924c49815533a8b9121c664599558a5d9ec51f8a1740a999"
+checksum = "a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726"
 dependencies = [
  "quote",
  "wasm-bindgen-macro-support",
@@ -2874,28 +2861,28 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.90"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bae1abb6806dc1ad9e560ed242107c0f6c84335f1749dd4e8ddb012ebd5e25a7"
+checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.90"
+version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4d91413b1c31d7539ba5ef2451af3f0b833a005eb27a631cec32bc0635a8602b"
+checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96"
 
 [[package]]
 name = "webpki-roots"
-version = "0.25.3"
+version = "0.25.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1778a42e8b3b90bff8d0f5032bf22250792889a5cdc752aa0020c84abe3aaf10"
+checksum = "5f20c57d8d7db6d3b86154206ae5d8fba62dd39573114de97c2cb0578251f8e1"
 
 [[package]]
 name = "which"
@@ -2927,11 +2914,11 @@ checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
 
 [[package]]
 name = "winapi-util"
-version = "0.1.6"
+version = "0.1.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596"
+checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
 dependencies = [
- "winapi",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -2946,7 +2933,7 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
 dependencies = [
- "windows-targets 0.52.4",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -2964,7 +2951,7 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
 dependencies = [
- "windows-targets 0.52.4",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -2984,17 +2971,18 @@ dependencies = [
 
 [[package]]
 name = "windows-targets"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7dd37b7e5ab9018759f893a1952c9420d060016fc19a472b4bb20d1bdd694d1b"
+checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
 dependencies = [
- "windows_aarch64_gnullvm 0.52.4",
- "windows_aarch64_msvc 0.52.4",
- "windows_i686_gnu 0.52.4",
- "windows_i686_msvc 0.52.4",
- "windows_x86_64_gnu 0.52.4",
- "windows_x86_64_gnullvm 0.52.4",
- "windows_x86_64_msvc 0.52.4",
+ "windows_aarch64_gnullvm 0.52.6",
+ "windows_aarch64_msvc 0.52.6",
+ "windows_i686_gnu 0.52.6",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc 0.52.6",
+ "windows_x86_64_gnu 0.52.6",
+ "windows_x86_64_gnullvm 0.52.6",
+ "windows_x86_64_msvc 0.52.6",
 ]
 
 [[package]]
@@ -3005,9 +2993,9 @@ checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
 
 [[package]]
 name = "windows_aarch64_gnullvm"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bcf46cf4c365c6f2d1cc93ce535f2c8b244591df96ceee75d8e83deb70a9cac9"
+checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
 
 [[package]]
 name = "windows_aarch64_msvc"
@@ -3017,9 +3005,9 @@ checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
 
 [[package]]
 name = "windows_aarch64_msvc"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da9f259dd3bcf6990b55bffd094c4f7235817ba4ceebde8e6d11cd0c5633b675"
+checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
 
 [[package]]
 name = "windows_i686_gnu"
@@ -3029,9 +3017,15 @@ checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
 
 [[package]]
 name = "windows_i686_gnu"
-version = "0.52.4"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
+
+[[package]]
+name = "windows_i686_gnullvm"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3"
+checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
 
 [[package]]
 name = "windows_i686_msvc"
@@ -3041,9 +3035,9 @@ checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
 
 [[package]]
 name = "windows_i686_msvc"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02"
+checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
 
 [[package]]
 name = "windows_x86_64_gnu"
@@ -3053,9 +3047,9 @@ checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
 
 [[package]]
 name = "windows_x86_64_gnu"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03"
+checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
@@ -3065,9 +3059,9 @@ checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177"
+checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
 
 [[package]]
 name = "windows_x86_64_msvc"
@@ -3077,9 +3071,9 @@ checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
 
 [[package]]
 name = "windows_x86_64_msvc"
-version = "0.52.4"
+version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8"
+checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
 
 [[package]]
 name = "winsafe"
@@ -3098,9 +3092,9 @@ dependencies = [
 
 [[package]]
 name = "xxhash-rust"
-version = "0.8.8"
+version = "0.8.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "53be06678ed9e83edb1745eb72efc0bbcd7b5c3c35711a860906aed827a13d61"
+checksum = "63658493314859b4dfdf3fb8c1defd61587839def09582db50b8a4e93afca6bb"
 
 [[package]]
 name = "xz2"
@@ -3131,47 +3125,47 @@ dependencies = [
 
 [[package]]
 name = "zerocopy"
-version = "0.7.32"
+version = "0.7.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be"
+checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0"
 dependencies = [
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.7.32"
+version = "0.7.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6"
+checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.68",
+ "syn 2.0.71",
 ]
 
 [[package]]
 name = "zstd"
-version = "0.13.0"
+version = "0.13.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bffb3309596d527cfcba7dfc6ed6052f1d39dfbd7c867aa2e865e4a449c10110"
+checksum = "fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9"
 dependencies = [
  "zstd-safe",
 ]
 
 [[package]]
 name = "zstd-safe"
-version = "7.0.0"
+version = "7.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "43747c7422e2924c11144d5229878b98180ef8b06cca4ab5af37afc8a8d8ea3e"
+checksum = "fa556e971e7b568dc775c136fc9de8c779b1c2fc3a63defaafadffdbd3181afa"
 dependencies = [
  "zstd-sys",
 ]
 
 [[package]]
 name = "zstd-sys"
-version = "2.0.9+zstd.1.5.5"
+version = "2.0.12+zstd.1.5.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9e16efa8a874a0481a574084d34cc26fdb3b99627480f785888deb6386506656"
+checksum = "0a4e40c320c3cb459d9a9ff6de98cff88f4751ee9275d140e2be94a2b74e4c13"
 dependencies = [
  "cc",
  "pkg-config",
diff --git a/Cargo.toml b/Cargo.toml
index 90c0e48..5fc39af 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "simpleaf"
-version = "0.17.1"
+version = "0.17.2"
 edition = "2021"
 authors = [
   "Rob Patro <rob@cs.umd.edu>",
@@ -36,13 +36,13 @@ seq_geom_parser = { git = "https://github.com/COMBINE-lab/seq_geom_parser", bran
 seq_geom_xform = { git = "https://github.com/COMBINE-lab/seq_geom_xform", branch = "dev", version = "0.4.0" }
 roers = { git = "https://github.com/COMBINE-lab/roers", branch = "main", version = "0.3.0" }
 anyhow = "^1.0"
-clap = { version = "4.5.8", features = ["derive", "cargo", "deprecated", "wrap_help", "help", "usage", "error-context"] } 
+clap = { version = "4.5.9", features = ["derive", "cargo", "deprecated", "wrap_help", "help", "usage", "error-context"] } 
 cmd_lib = "^1.9.4"
 tracing = "0.1.40"
 tracing-subscriber = { version = "0.3.18", default-features = true, features = ["env-filter"] }
 semver = "^1.0.23"
-serde = {version = "1.0.203", features = ["derive"]}
-serde_json = "1.0.119"
+serde = {version = "1.0.204", features = ["derive"]}
+serde_json = "1.0.120"
 time = {version = "^0.3.36", features = ["macros", "formatting", "parsing", "serde", "serde-human-readable"]}
 which = "^6.0.1"
 jrsonnet-evaluator = "0.5.0-pre95"
diff --git a/simpleaf_conda_env.yml b/simpleaf_conda_env.yml
index 0ef72b2..eaed75b 100644
--- a/simpleaf_conda_env.yml
+++ b/simpleaf_conda_env.yml
@@ -8,5 +8,5 @@ channels:
 dependencies:
   - libboost>=1.85.0
   - salmon>=1.10.3
-  - alevin-fry>=0.8.2
+  - alevin-fry>=0.10.0
   - piscem>=0.10.0