From faffad63b57e42eba76b75d886745ef45cfc2ef0 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Tue, 19 Nov 2024 11:26:41 +0100
Subject: [PATCH] fix: refactor csq analysis code (#599)

---
 .gitattributes                                |   1 +
 Cargo.lock                                    | 890 +++++++++-------
 src/annotate/seqvars/csq.rs                   | 990 ++++++++++++------
 ...snv_brca1_one_variant@17-41197818-G-C.snap |   5 +
 ...snv_brca1_one_variant@17-41197819-G-C.snap |   5 +
 ...38-ensembl.disagreement-subset.txs.bin.zst |   3 +
 .../vep.disagreement-cases.expected.vcf       |   3 +
 .../seqvars/vep.disagreement-cases.vcf        |   3 +
 8 files changed, 1199 insertions(+), 701 deletions(-)
 create mode 100644 tests/data/annotate/db/grch38/GRCh38-ensembl.disagreement-subset.txs.bin.zst
 create mode 100644 tests/data/annotate/seqvars/vep.disagreement-cases.expected.vcf
 create mode 100644 tests/data/annotate/seqvars/vep.disagreement-cases.vcf

diff --git a/.gitattributes b/.gitattributes
index 093d1062..1c455953 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -4,3 +4,4 @@ tests/data/vars/*.tsv* filter=lfs diff=lfs merge=lfs -text
 tests/data/** filter=lfs diff=lfs merge=lfs -text
 *.bin filter=lfs diff=lfs merge=lfs -text
 src/db/create/snapshots/mehari__db__create__test__run_smoke_brca1_opa1.snap filter=lfs diff=lfs merge=lfs -text
+tests/data/annotate/db/grch38/GRCh38-ensembl.disagreement-subset.txs.bin.zst filter=lfs diff=lfs merge=lfs -text
diff --git a/Cargo.lock b/Cargo.lock
index 1e97afc7..f115b041 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -21,9 +21,9 @@ dependencies = [
 
 [[package]]
 name = "actix-http"
-version = "3.8.0"
+version = "3.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3ae682f693a9cd7b058f2b0b5d9a6d7728a8555779bedbbc35dd88528611d020"
+checksum = "d48f96fc3003717aeb9856ca3d02a8c7de502667ad76eeacd830b48d2e91fac4"
 dependencies = [
  "actix-codec",
  "actix-rt",
@@ -65,7 +65,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e01ed3140b2f8d422c68afa1ed2e85d996ea619c988ac834d255db32138655cb"
 dependencies = [
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -182,24 +182,18 @@ dependencies = [
  "actix-router",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
 name = "addr2line"
-version = "0.22.0"
+version = "0.24.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678"
+checksum = "dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1"
 dependencies = [
  "gimli",
 ]
 
-[[package]]
-name = "adler"
-version = "1.0.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
-
 [[package]]
 name = "adler2"
 version = "2.0.0"
@@ -256,9 +250,9 @@ dependencies = [
 
 [[package]]
 name = "allocator-api2"
-version = "0.2.18"
+version = "0.2.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5c6cb57a04249c6480766f7f7cef5467412af1490f8d1e243141daddada3264f"
+checksum = "45862d1c77f2228b9e10bc609d5bc203d86ebc9b87ad8d5d5167a6c9abf739d9"
 
 [[package]]
 name = "android-tzdata"
@@ -330,9 +324,9 @@ dependencies = [
 
 [[package]]
 name = "anstream"
-version = "0.6.15"
+version = "0.6.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "64e15c1ab1f89faffbf04a634d5e1962e9074f2741eef6d97f3c4e322426d526"
+checksum = "8acc5369981196006228e28809f761875c0327210a891e941f4c683b3a99529b"
 dependencies = [
  "anstyle",
  "anstyle-parse",
@@ -345,36 +339,36 @@ dependencies = [
 
 [[package]]
 name = "anstyle"
-version = "1.0.8"
+version = "1.0.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1"
+checksum = "55cc3b69f167a1ef2e161439aa98aed94e6028e5f9a59be9a6ffb47aef1651f9"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.5"
+version = "0.2.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "eb47de1e80c2b463c735db5b217a0ddc39d612e7ac9e2e96a5aed1f57616c1cb"
+checksum = "3b2d16507662817a6a20a9ea92df6652ee4f94f914589377d69f3b21bc5798a9"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.1.1"
+version = "1.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6d36fc52c7f6c869915e99412912f22093507da8d9e942ceaf66fe4b7c14422a"
+checksum = "79947af37f4177cfead1110013d678905c37501914fba0efea834c3fe9a8d60c"
 dependencies = [
- "windows-sys 0.52.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.4"
+version = "3.0.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5bf74e1b6e971609db8ca7a9ce79fd5768ab6ae46441c572e46cf596f59e57f8"
+checksum = "2109dbce0e72be3ec00bed26e6a7479ca384ad226efdd66db8fa2e3a38c83125"
 dependencies = [
  "anstyle",
- "windows-sys 0.52.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
@@ -394,18 +388,18 @@ dependencies = [
 
 [[package]]
 name = "arbitrary"
-version = "1.3.2"
+version = "1.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7d5a26814d8dcb93b0e5a0ff3c6d80a8843bafb21b39e8e18a6f05471870e110"
+checksum = "dde20b3d026af13f561bdd0f15edf01fc734f0dafcedbaf42bba506a9517f223"
 dependencies = [
  "derive_arbitrary",
 ]
 
 [[package]]
 name = "arrayvec"
-version = "0.7.4"
+version = "0.7.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "96d30a06541fbafbc7f82ed10c06164cfbd2c401138f6addd8404629c4b16711"
+checksum = "7c02d123df017efcdfbd739ef81735b36c5ba83ec3c59c80a9d7ecc718f92e50"
 
 [[package]]
 name = "async-attributes"
@@ -455,9 +449,9 @@ dependencies = [
 
 [[package]]
 name = "async-executor"
-version = "1.13.0"
+version = "1.13.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d7ebdfa2ebdab6b1760375fa7d6f382b9f486eac35fc994625a00e89280bdbb7"
+checksum = "30ca9a001c1e8ba5149f91a74362376cc6bc5b919d92d988668657bd570bdcec"
 dependencies = [
  "async-task",
  "concurrent-queue",
@@ -483,9 +477,9 @@ dependencies = [
 
 [[package]]
 name = "async-io"
-version = "2.3.3"
+version = "2.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0d6baa8f0178795da0e71bc42c9e5d13261aac7ee549853162e66a241ba17964"
+checksum = "43a2b323ccce0a1d90b449fd71f2a06ca7faa7c54c2751f06c9bd851fc061059"
 dependencies = [
  "async-lock",
  "cfg-if",
@@ -497,7 +491,7 @@ dependencies = [
  "rustix",
  "slab",
  "tracing",
- "windows-sys 0.52.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
@@ -546,13 +540,13 @@ checksum = "8b75356056920673b02621b35afd0f7dda9306d03c79a30f5c56c44cf256e3de"
 
 [[package]]
 name = "async-trait"
-version = "0.1.81"
+version = "0.1.83"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6e0c28dcc82d7c8ead5cb13beb15405b57b8546e93215673ff8ca0349a028107"
+checksum = "721cae7de5c34fbb2acd27e21e6d2cf7b886dce0c27388d46c4e6c47ea4318dd"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -563,23 +557,23 @@ checksum = "1505bd5d3d116872e7271a6d4e16d81d0c8570876c8de68093a09ac269d8aac0"
 
 [[package]]
 name = "autocfg"
-version = "1.3.0"
+version = "1.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
+checksum = "ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26"
 
 [[package]]
 name = "backtrace"
-version = "0.3.73"
+version = "0.3.74"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5cc23269a4f8976d0a4d2e7109211a419fe30e8d88d677cd60b6bc79c5732e0a"
+checksum = "8d82cb332cdfaed17ae235a638438ac4d4839913cc2af585c3c6746e8f8bee1a"
 dependencies = [
  "addr2line",
- "cc",
  "cfg-if",
  "libc",
- "miniz_oxide 0.7.4",
+ "miniz_oxide",
  "object",
  "rustc-demangle",
+ "windows-targets",
 ]
 
 [[package]]
@@ -614,9 +608,9 @@ dependencies = [
 
 [[package]]
 name = "bindgen"
-version = "0.69.4"
+version = "0.69.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a00dc851838a2120612785d195287475a3ac45514741da670b735818822129a0"
+checksum = "271383c67ccabffb7381723dea0672a673f292304fcb45c01cc648c7a8d58088"
 dependencies = [
  "bitflags 2.6.0",
  "cexpr",
@@ -629,7 +623,7 @@ dependencies = [
  "regex",
  "rustc-hash 1.1.0",
  "shlex",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -773,9 +767,9 @@ checksum = "c057a3e5631e754d98c5a9e3baa56803fce8fe238b009ecd876e57d381d44c00"
 
 [[package]]
 name = "borsh"
-version = "1.5.1"
+version = "1.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a6362ed55def622cddc70a4746a68554d7b687713770de539e59a739b249f8ed"
+checksum = "f5327f6c99920069d1fe374aa743be1af0031dea9f250852cdf1ae6a0861ee24"
 dependencies = [
  "borsh-derive",
  "cfg_aliases",
@@ -783,16 +777,15 @@ dependencies = [
 
 [[package]]
 name = "borsh-derive"
-version = "1.5.1"
+version = "1.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c3ef8005764f53cd4dca619f5bf64cafd4664dada50ece25e4d81de54c80cc0b"
+checksum = "10aedd8f1a81a8aafbfde924b0e3061cd6fedd6f6bbcfc6a76e6fd426d7bfe26"
 dependencies = [
  "once_cell",
  "proc-macro-crate",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
- "syn_derive",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -895,9 +888,9 @@ checksum = "5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce"
 
 [[package]]
 name = "bytemuck"
-version = "1.16.3"
+version = "1.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "102087e286b4677862ea56cf8fc58bb2cdfa8725c40ffb80fe3a008eb7f2fc83"
+checksum = "8334215b81e418a0a7bdb8ef0849474f40bb10c8b71f1c4ed315cff49f32494d"
 
 [[package]]
 name = "byteorder"
@@ -907,9 +900,9 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bytes"
-version = "1.7.1"
+version = "1.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8318a53db07bb3f8dca91a600466bdb3f2eaadeedfdbcf02e1accbad9271ba50"
+checksum = "9ac0150caa2ae65ca5bd83f25c7de183dea78d4d366469f148435e2acfbad0da"
 
 [[package]]
 name = "bytestring"
@@ -965,7 +958,7 @@ dependencies = [
  "darling",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -995,12 +988,13 @@ checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5"
 
 [[package]]
 name = "cc"
-version = "1.1.7"
+version = "1.1.37"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26a5c3fd7bfa1ce3897a3a3501d362b2d87b7f2583ebcb4a949ec25911025cbc"
+checksum = "40545c26d092346d8a8dab71ee48e7685a7a9cba76e634790c215b41a4a7b4cf"
 dependencies = [
  "jobserver",
  "libc",
+ "shlex",
 ]
 
 [[package]]
@@ -1118,7 +1112,7 @@ dependencies = [
  "heck",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1129,9 +1123,9 @@ checksum = "1462739cb27611015575c0c11df5df7601141071f07518d56fcc1be504cbec97"
 
 [[package]]
 name = "colorchoice"
-version = "1.0.2"
+version = "1.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d3fd119d74b830634cea2a0f58bbd0d54540518a14397557951e79340abc28c0"
+checksum = "5b63caa9aa9397e2d9480a9b13673856c78d8ac123288526c37d7839f2a86990"
 
 [[package]]
 name = "concurrent-queue"
@@ -1183,9 +1177,9 @@ dependencies = [
 
 [[package]]
 name = "core-foundation-sys"
-version = "0.8.6"
+version = "0.8.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
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+checksum = "773648b94d0e5d620f64f280777445740e61fe701025087ec8b57f45c791888b"
 
 [[package]]
 name = "coz"
@@ -1199,18 +1193,18 @@ dependencies = [
 
 [[package]]
 name = "cpp_demangle"
-version = "0.4.3"
+version = "0.4.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7e8227005286ec39567949b33df9896bcadfa6051bccca2488129f108ca23119"
+checksum = "96e58d342ad113c2b878f16d5d034c03be492ae460cdbc02b7f0f2284d310c7d"
 dependencies = [
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 ]
 
 [[package]]
 name = "cpufeatures"
-version = "0.2.12"
+version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "53fe5e26ff1b7aef8bca9c6080520cfb8d9333c7568e1829cef191a9723e5504"
+checksum = "0ca741a962e1b0bff6d724a1a0958b686406e853bb14061f218562e1896f95e6"
 dependencies = [
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 ]
@@ -1360,7 +1354,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "strsim",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1371,7 +1365,7 @@ checksum = "d336a2a514f6ccccaa3e09b02d41d35330c07ddf03a62165fcec10bb561c7806"
 dependencies = [
  "darling_core",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1411,7 +1405,7 @@ checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1422,18 +1416,18 @@ checksum = "2cdc8d50f426189eef89dac62fabfa0abb27d5cc008f25bf4156a0203325becc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
 name = "derive_arbitrary"
-version = "1.3.2"
+version = "1.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "67e77553c4162a157adbf834ebae5b415acbecbeafc7a74b0e886657506a7611"
+checksum = "30542c1ad912e0e3d22a1935c290e12e8a29d704a420177a31faad4a601a0800"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1454,7 +1448,7 @@ dependencies = [
  "darling",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1464,7 +1458,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ab63b0e2bf4d5928aff72e83a7dace85d7bba5fe12dcc3c5a572d78caffd3f3c"
 dependencies = [
  "derive_builder_core",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1477,7 +1471,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustc_version 0.4.1",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1521,7 +1515,7 @@ checksum = "97369cbbc041bc366949bc74d34658d6cda5621039731c6310521892a3a20ae0"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1544,9 +1538,9 @@ checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f"
 
 [[package]]
 name = "encoding_rs"
-version = "0.8.34"
+version = "0.8.35"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b45de904aa0b010bce2ab45264d0631681847fa7b6f2eaa7dab7619943bc4f59"
+checksum = "75030f3c4f45dafd7586dd6780965a8c7e8e285a5ecb86713e63a79c5b2766f3"
 dependencies = [
  "cfg-if",
 ]
@@ -1569,7 +1563,7 @@ checksum = "f282cfdfe92516eb26c2af8589c274c7c17681f5ecc03c18255fe741c6aa64eb"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1590,7 +1584,7 @@ checksum = "de0d48a183585823424a4ce1aa132d174a6a81bd540895822eb4c8373a8e49e8"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1689,9 +1683,9 @@ checksum = "7360491ce676a36bf9bb3c56c1aa791658183a54d2744120f27285738d90465a"
 
 [[package]]
 name = "fastrand"
-version = "2.1.1"
+version = "2.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e8c02a5121d4ea3eb16a80748c74f5549a5665e4c21333c6098f283870fbdea6"
+checksum = "486f806e73c5707928240ddc295403b1b93c96a02038563881c4a2fd84b81ac4"
 
 [[package]]
 name = "feature-probe"
@@ -1724,7 +1718,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a1b589b4dc103969ad3cf85c950899926ec64300a1a46d76c03a6072957036f0"
 dependencies = [
  "crc32fast",
- "miniz_oxide 0.8.0",
+ "miniz_oxide",
 ]
 
 [[package]]
@@ -1798,9 +1792,9 @@ checksum = "9e5c1b78ca4aae1ac06c48a526a655760685149f0d465d21f37abfe57ce075c6"
 
 [[package]]
 name = "futures-lite"
-version = "2.3.0"
+version = "2.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "52527eb5074e35e9339c6b4e8d12600c7128b68fb25dcb9fa9dec18f7c25f3a5"
+checksum = "cef40d21ae2c515b51041df9ed313ed21e572df340ea58a922a0aefe7e8891a1"
 dependencies = [
  "fastrand",
  "futures-core",
@@ -1817,7 +1811,7 @@ checksum = "162ee34ebcb7c64a8abebc059ce0fee27c2262618d7b60ed8faf72fef13c3650"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1888,9 +1882,9 @@ dependencies = [
 
 [[package]]
 name = "gimli"
-version = "0.29.0"
+version = "0.31.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "40ecd4077b5ae9fd2e9e169b102c6c330d0605168eb0e8bf79952b256dbefffd"
+checksum = "07e28edb80900c19c28f1072f2e8aeca7fa06b23cd4169cefe1af5aa3260783f"
 
 [[package]]
 name = "git2"
@@ -1973,9 +1967,9 @@ dependencies = [
 
 [[package]]
 name = "hashbrown"
-version = "0.15.0"
+version = "0.15.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1e087f84d4f86bf4b218b927129862374b72199ae7d8657835f1e89000eea4fb"
+checksum = "3a9bfc1af68b1726ea47d3d5109de126281def866b33970e10fbab11b5dafab3"
 
 [[package]]
 name = "hashlink"
@@ -2095,9 +2089,9 @@ dependencies = [
 
 [[package]]
 name = "httparse"
-version = "1.9.4"
+version = "1.9.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0fcc0b4a115bf80b728eb8ea024ad5bd707b615bfed49e0665b6e0f86fd082d9"
+checksum = "7d71d3574edd2771538b901e6549113b4006ece66150fb69c0fb6d9a2adae946"
 
 [[package]]
 name = "httpdate"
@@ -2119,9 +2113,9 @@ checksum = "a17b27f28a7466846baca75f0a5244e546e44178eb7f1c07a3820f413e91c6b0"
 
 [[package]]
 name = "hyper"
-version = "1.4.1"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "50dfd22e0e76d0f662d429a5f80fcaf3855009297eab6a0a9f8543834744ba05"
+checksum = "bbbff0a806a4728c99295b254c8838933b5b082d75e3cb70c8dab21fdfbcfa9a"
 dependencies = [
  "bytes",
  "futures-channel",
@@ -2156,9 +2150,9 @@ dependencies = [
 
 [[package]]
 name = "hyper-util"
-version = "0.1.8"
+version = "0.1.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da62f120a8a37763efb0cf8fdf264b884c7b8b9ac8660b900c8661030c00e6ba"
+checksum = "df2dcfbe0677734ab2f3ffa7fa7bfd4706bfdc1ef393f2ee30184aed67e631b4"
 dependencies = [
  "bytes",
  "futures-channel",
@@ -2169,16 +2163,15 @@ dependencies = [
  "pin-project-lite",
  "socket2",
  "tokio",
- "tower",
  "tower-service",
  "tracing",
 ]
 
 [[package]]
 name = "iana-time-zone"
-version = "0.1.60"
+version = "0.1.61"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e7ffbb5a1b541ea2561f8c41c087286cc091e21e556a4f09a8f6cbf17b69b141"
+checksum = "235e081f3925a06703c2d0117ea8b91f042756fd6e7a6e5d901e8ca1a996b220"
 dependencies = [
  "android_system_properties",
  "core-foundation-sys",
@@ -2197,6 +2190,124 @@ dependencies = [
  "cc",
 ]
 
+[[package]]
+name = "icu_collections"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "db2fa452206ebee18c4b5c2274dbf1de17008e874b4dc4f0aea9d01ca79e4526"
+dependencies = [
+ "displaydoc",
+ "yoke",
+ "zerofrom",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_locid"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "13acbb8371917fc971be86fc8057c41a64b521c184808a698c02acc242dbf637"
+dependencies = [
+ "displaydoc",
+ "litemap",
+ "tinystr",
+ "writeable",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_locid_transform"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "01d11ac35de8e40fdeda00d9e1e9d92525f3f9d887cdd7aa81d727596788b54e"
+dependencies = [
+ "displaydoc",
+ "icu_locid",
+ "icu_locid_transform_data",
+ "icu_provider",
+ "tinystr",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_locid_transform_data"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fdc8ff3388f852bede6b579ad4e978ab004f139284d7b28715f773507b946f6e"
+
+[[package]]
+name = "icu_normalizer"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "19ce3e0da2ec68599d193c93d088142efd7f9c5d6fc9b803774855747dc6a84f"
+dependencies = [
+ "displaydoc",
+ "icu_collections",
+ "icu_normalizer_data",
+ "icu_properties",
+ "icu_provider",
+ "smallvec",
+ "utf16_iter",
+ "utf8_iter",
+ "write16",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_normalizer_data"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f8cafbf7aa791e9b22bec55a167906f9e1215fd475cd22adfcf660e03e989516"
+
+[[package]]
+name = "icu_properties"
+version = "1.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "93d6020766cfc6302c15dbbc9c8778c37e62c14427cb7f6e601d849e092aeef5"
+dependencies = [
+ "displaydoc",
+ "icu_collections",
+ "icu_locid_transform",
+ "icu_properties_data",
+ "icu_provider",
+ "tinystr",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_properties_data"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "67a8effbc3dd3e4ba1afa8ad918d5684b8868b3b26500753effea8d2eed19569"
+
+[[package]]
+name = "icu_provider"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6ed421c8a8ef78d3e2dbc98a973be2f3770cb42b606e3ab18d6237c4dfde68d9"
+dependencies = [
+ "displaydoc",
+ "icu_locid",
+ "icu_provider_macros",
+ "stable_deref_trait",
+ "tinystr",
+ "writeable",
+ "yoke",
+ "zerofrom",
+ "zerovec",
+]
+
+[[package]]
+name = "icu_provider_macros"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1ec89e9337638ecdc08744df490b221a7399bf8d164eb52a665454e60e075ad6"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.87",
+]
+
 [[package]]
 name = "ident_case"
 version = "1.0.1"
@@ -2205,19 +2316,30 @@ checksum = "b9e0384b61958566e926dc50660321d12159025e767c18e043daf26b70104c39"
 
 [[package]]
 name = "idna"
-version = "0.5.0"
+version = "1.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "634d9b1461af396cad843f47fdba5597a4f9e6ddd4bfb6ff5d85028c25cb12f6"
+checksum = "686f825264d630750a544639377bae737628043f20d38bbc029e8f29ea968a7e"
 dependencies = [
- "unicode-bidi",
- "unicode-normalization",
+ "idna_adapter",
+ "smallvec",
+ "utf8_iter",
+]
+
+[[package]]
+name = "idna_adapter"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "daca1df1c957320b2cf139ac61e7bd64fed304c5040df000a745aa1de3b4ef71"
+dependencies = [
+ "icu_normalizer",
+ "icu_properties",
 ]
 
 [[package]]
 name = "impl-more"
-version = "0.1.6"
+version = "0.1.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "206ca75c9c03ba3d4ace2460e57b189f39f43de612c2f85836e65c929701bb2d"
+checksum = "aae21c3177a27788957044151cc2800043d127acaa460a47ebb9b84dfa2c6aa0"
 
 [[package]]
 name = "indexmap"
@@ -2226,7 +2348,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "707907fe3c25f5424cce2cb7e1cbcafee6bdbe735ca90ef77c29e84591e5b9da"
 dependencies = [
  "equivalent",
- "hashbrown 0.15.0",
+ "hashbrown 0.15.1",
  "serde",
 ]
 
@@ -2286,17 +2408,17 @@ dependencies = [
 
 [[package]]
 name = "ipnet"
-version = "2.10.0"
+version = "2.10.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "187674a687eed5fe42285b40c6291f9a01517d415fad1c3cbc6a9f778af7fcd4"
+checksum = "ddc24109865250148c2e0f3d25d4f0f479571723792d3802153c60922a4fb708"
 
 [[package]]
 name = "is-terminal"
-version = "0.4.12"
+version = "0.4.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b"
+checksum = "261f68e344040fbd0edea105bef17c66edf46f984ddb1115b775ce31be948f4b"
 dependencies = [
- "hermit-abi 0.3.9",
+ "hermit-abi 0.4.0",
  "libc",
  "windows-sys 0.52.0",
 ]
@@ -2360,9 +2482,9 @@ dependencies = [
 
 [[package]]
 name = "js-sys"
-version = "0.3.69"
+version = "0.3.72"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "29c15563dc2726973df627357ce0c9ddddbea194836909d655df6a75d2cf296d"
+checksum = "6a88f1bda2bd75b0452a14784937d796722fdebfe50df998aeb3f0b7603019a9"
 dependencies = [
  "wasm-bindgen",
 ]
@@ -2396,7 +2518,7 @@ dependencies = [
  "convert_case 0.6.0",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -2492,9 +2614,9 @@ dependencies = [
 
 [[package]]
 name = "libc"
-version = "0.2.158"
+version = "0.2.162"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d8adc4bb1803a324070e64a98ae98f38934d91957a99cfb3a43dcbc01bc56439"
+checksum = "18d287de67fe55fd7e1581fe933d965a5a9477b38e949cfa9f8574ef01506398"
 
 [[package]]
 name = "libgit2-sys"
@@ -2520,9 +2642,9 @@ dependencies = [
 
 [[package]]
 name = "libm"
-version = "0.2.8"
+version = "0.2.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
+checksum = "8355be11b20d696c8f18f6cc018c4e372165b1fa8126cef092399c9951984ffa"
 
 [[package]]
 name = "librocksdb-sys"
@@ -2552,9 +2674,9 @@ dependencies = [
 
 [[package]]
 name = "libz-sys"
-version = "1.1.18"
+version = "1.1.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c15da26e5af7e25c90b37a2d75cdbf940cf4a55316de9d84c679c9b8bfabf82e"
+checksum = "d2d16453e800a8cf6dd2fc3eb4bc99b786a9b90c663b8559a5b1a041bf89e472"
 dependencies = [
  "cc",
  "libc",
@@ -2574,6 +2696,12 @@ version = "0.4.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89"
 
+[[package]]
+name = "litemap"
+version = "0.7.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "643cb0b8d4fcc284004d5fd0d67ccf61dfffadb7f75e1e71bc420f4688a3a704"
+
 [[package]]
 name = "local-channel"
 version = "0.1.5"
@@ -2612,9 +2740,9 @@ dependencies = [
 
 [[package]]
 name = "lz4-sys"
-version = "1.10.0"
+version = "1.11.1+lz4-1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "109de74d5d2353660401699a4174a4ff23fcc649caf553df71933c7fb45ad868"
+checksum = "6bd8c0d6c6ed0cd30b3652886bb8711dc4bb01d637a68105a3d5158039b418e6"
 dependencies = [
  "cc",
  "libc",
@@ -2746,9 +2874,9 @@ checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "memmap2"
-version = "0.9.4"
+version = "0.9.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fe751422e4a8caa417e13c3ea66452215d7d63e19e604f4980461212f3ae1322"
+checksum = "fd3f7eed9d3848f8b98834af67102b720745c4ec028fcd0aa0239277e7de374f"
 dependencies = [
  "libc",
 ]
@@ -2775,15 +2903,6 @@ version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
 
-[[package]]
-name = "miniz_oxide"
-version = "0.7.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b8a240ddb74feaf34a79a7add65a741f3167852fba007066dcac1ca548d89c08"
-dependencies = [
- "adler",
-]
-
 [[package]]
 name = "miniz_oxide"
 version = "0.8.0"
@@ -2801,9 +2920,9 @@ checksum = "9bec4598fddb13cc7b528819e697852653252b760f1228b7642679bf2ff2cd07"
 
 [[package]]
 name = "mio"
-version = "1.0.1"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4569e456d394deccd22ce1c1913e6ea0e54519f577285001215d33557431afe4"
+checksum = "80e04d1dcff3aae0704555fe5fee3bcfaf3d1fdf8a7e521d5b9d2b42acb52cec"
 dependencies = [
  "hermit-abi 0.3.9",
  "libc",
@@ -2847,19 +2966,21 @@ checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
 name = "ndarray"
-version = "0.15.6"
+version = "0.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32"
+checksum = "882ed72dce9365842bf196bdeedf5055305f11fc8c03dee7bb0194a6cad34841"
 dependencies = [
  "matrixmultiply",
  "num-complex",
  "num-integer",
  "num-traits",
+ "portable-atomic",
+ "portable-atomic-util",
  "rawpointer",
 ]
 
@@ -3230,7 +3351,7 @@ dependencies = [
  "proc-macro-crate",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -3258,15 +3379,15 @@ dependencies = [
  "kinded",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
  "urlencoding",
 ]
 
 [[package]]
 name = "object"
-version = "0.36.3"
+version = "0.36.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "27b64972346851a39438c60b341ebc01bba47464ae329e55cf343eb93964efd9"
+checksum = "aedf0a2d09c573ed1d8d85b30c119153926a2b36dce0ab28322c09a117a4683e"
 dependencies = [
  "memchr",
 ]
@@ -3285,9 +3406,9 @@ checksum = "b410bbe7e14ab526a0e86877eb47c6996a2bd7746f027ba551028c925390e4e9"
 
 [[package]]
 name = "ordered-float"
-version = "4.2.2"
+version = "4.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4a91171844676f8c7990ce64959210cd2eaef32c2612c50f9fae9f8aaa6065a6"
+checksum = "c65ee1f9701bf938026630b455d5315f490640234259037edb259798b3bcf85e"
 dependencies = [
  "num-traits",
 ]
@@ -3300,9 +3421,9 @@ checksum = "b15813163c1d831bf4a13c3610c05c0d03b39feb07f7e09fa234dac9b15aaf39"
 
 [[package]]
 name = "parking"
-version = "2.2.0"
+version = "2.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bb813b8af86854136c6922af0598d719255ecb2179515e6e7730d468f05c9cae"
+checksum = "f38d5652c16fde515bb1ecef450ab0f6a219d619a7274976324d5e377f7dceba"
 
 [[package]]
 name = "parking_lot"
@@ -3322,7 +3443,7 @@ checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
 dependencies = [
  "cfg-if",
  "libc",
- "redox_syscall 0.5.3",
+ "redox_syscall",
  "smallvec",
  "windows-targets",
 ]
@@ -3335,7 +3456,7 @@ checksum = "287d8d3ebdce117b8539f59411e4ed9ec226e0a4153c7f55495c6070d68e6f72"
 dependencies = [
  "parse-display-derive",
  "regex",
- "regex-syntax 0.8.4",
+ "regex-syntax 0.8.5",
 ]
 
 [[package]]
@@ -3347,9 +3468,9 @@ dependencies = [
  "proc-macro2",
  "quote",
  "regex",
- "regex-syntax 0.8.4",
+ "regex-syntax 0.8.5",
  "structmeta",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -3429,31 +3550,11 @@ dependencies = [
  "siphasher",
 ]
 
-[[package]]
-name = "pin-project"
-version = "1.1.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b6bf43b791c5b9e34c3d182969b4abb522f9343702850a2e57f460d00d09b4b3"
-dependencies = [
- "pin-project-internal",
-]
-
-[[package]]
-name = "pin-project-internal"
-version = "1.1.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2f38a4412a78282e09a2cf38d195ea5420d15ba0602cb375210efbc877243965"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.85",
-]
-
 [[package]]
 name = "pin-project-lite"
-version = "0.2.14"
+version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bda66fc9667c18cb2758a2ac84d1167245054bcf85d5d1aaa6923f45801bdd02"
+checksum = "915a1e146535de9163f3987b8944ed8cf49a18bb0056bcebcdcece385cece4ff"
 
 [[package]]
 name = "pin-utils"
@@ -3463,9 +3564,9 @@ checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184"
 
 [[package]]
 name = "piper"
-version = "0.2.3"
+version = "0.2.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae1d5c74c9876f070d3e8fd503d748c7d974c3e48da8f41350fa5222ef9b4391"
+checksum = "96c8c490f422ef9a4efd2cb5b42b76c8613d7e7dfc1caf667b8a3350a5acc066"
 dependencies = [
  "atomic-waker",
  "fastrand",
@@ -3474,15 +3575,15 @@ dependencies = [
 
 [[package]]
 name = "pkg-config"
-version = "0.3.30"
+version = "0.3.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec"
+checksum = "953ec861398dccce10c670dfeaf3ec4911ca479e9c02154b3a215178c5f566f2"
 
 [[package]]
 name = "plotters"
-version = "0.3.6"
+version = "0.3.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a15b6eccb8484002195a3e44fe65a4ce8e93a625797a063735536fd59cb01cf3"
+checksum = "5aeb6f403d7a4911efb1e33402027fc44f29b5bf6def3effcc22d7bb75f2b747"
 dependencies = [
  "num-traits",
  "plotters-backend",
@@ -3493,24 +3594,24 @@ dependencies = [
 
 [[package]]
 name = "plotters-backend"
-version = "0.3.6"
+version = "0.3.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "414cec62c6634ae900ea1c56128dfe87cf63e7caece0852ec76aba307cebadb7"
+checksum = "df42e13c12958a16b3f7f4386b9ab1f3e7933914ecea48da7139435263a4172a"
 
 [[package]]
 name = "plotters-svg"
-version = "0.3.6"
+version = "0.3.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "81b30686a7d9c3e010b84284bdd26a29f2138574f52f5eb6f794fc0ad924e705"
+checksum = "51bae2ac328883f7acdfea3d66a7c35751187f870bc81f94563733a154d7a670"
 dependencies = [
  "plotters-backend",
 ]
 
 [[package]]
 name = "polling"
-version = "3.7.2"
+version = "3.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a3ed00ed3fbf728b5816498ecd316d1716eecaced9c0c8d2c5a6740ca214985b"
+checksum = "a604568c3202727d1507653cb121dbd627a58684eb09a820fd746bee38b4442f"
 dependencies = [
  "cfg-if",
  "concurrent-queue",
@@ -3518,20 +3619,29 @@ dependencies = [
  "pin-project-lite",
  "rustix",
  "tracing",
- "windows-sys 0.52.0",
+ "windows-sys 0.59.0",
 ]
 
 [[package]]
 name = "portable-atomic"
-version = "1.7.0"
+version = "1.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cc9c68a3f6da06753e9335d63e27f6b9754dd1920d941135b7ea8224f141adb2"
+
+[[package]]
+name = "portable-atomic-util"
+version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da544ee218f0d287a911e9c99a39a8c9bc8fcad3cb8db5959940044ecfc67265"
+checksum = "90a7d5beecc52a491b54d6dd05c7a45ba1801666a5baad9fdbfc6fef8d2d206c"
+dependencies = [
+ "portable-atomic",
+]
 
 [[package]]
 name = "postgres"
-version = "0.19.8"
+version = "0.19.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c9ec84ab55b0f9e418675de50052d494ba893fd28c65769a6e68fcdacbee2b8"
+checksum = "95c918733159f4d55d2ceb262950f00b0aebd6af4aa97b5a47bb0655120475ed"
 dependencies = [
  "bytes",
  "fallible-iterator 0.2.0",
@@ -3561,9 +3671,9 @@ dependencies = [
 
 [[package]]
 name = "postgres-types"
-version = "0.2.7"
+version = "0.2.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02048d9e032fb3cc3413bbf7b83a15d84a5d419778e2628751896d856498eee9"
+checksum = "f66ea23a2d0e5734297357705193335e0a957696f34bed2f2faefacb2fec336f"
 dependencies = [
  "bytes",
  "chrono",
@@ -3619,12 +3729,12 @@ dependencies = [
 
 [[package]]
 name = "prettyplease"
-version = "0.2.20"
+version = "0.2.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5f12335488a2f3b0a83b14edad48dca9879ce89b2edd10e80237e4e852dd645e"
+checksum = "64d1ec885c64d0457d564db4ec299b2dae3f9c02808b8ad9c3a089c591b18033"
 dependencies = [
  "proc-macro2",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -3662,9 +3772,9 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.86"
+version = "1.0.89"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77"
+checksum = "f139b0662de085916d1fb67d2b4169d1addddda1919e696f3252b740b629986e"
 dependencies = [
  "unicode-ident",
 ]
@@ -3721,7 +3831,7 @@ dependencies = [
  "prost",
  "prost-types",
  "regex",
- "syn 2.0.85",
+ "syn 2.0.87",
  "tempfile",
 ]
 
@@ -3735,7 +3845,7 @@ dependencies = [
  "itertools 0.13.0",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -3825,10 +3935,11 @@ dependencies = [
 
 [[package]]
 name = "quinn-udp"
-version = "0.5.5"
+version = "0.5.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4fe68c2e9e1a1234e218683dbdf9f9dfcb094113c5ac2b938dfcb9bab4c4140b"
+checksum = "7d5a626c6807713b15cac82a6acaccd6043c9a5408c24baae07611fec3f243da"
 dependencies = [
+ "cfg_aliases",
  "libc",
  "once_cell",
  "socket2",
@@ -3919,32 +4030,23 @@ dependencies = [
 
 [[package]]
 name = "redox_syscall"
-version = "0.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
-dependencies = [
- "bitflags 1.3.2",
-]
-
-[[package]]
-name = "redox_syscall"
-version = "0.5.3"
+version = "0.5.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2a908a6e00f1fdd0dfd9c0eb08ce85126f6d8bbda50017e74bc4a4b7d4a926a4"
+checksum = "9b6dfecf2c74bce2466cabf93f6664d6998a69eb21e39f4207930065b27b771f"
 dependencies = [
  "bitflags 2.6.0",
 ]
 
 [[package]]
 name = "regex"
-version = "1.10.6"
+version = "1.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4219d74c6b67a3654a9fbebc4b419e22126d13d2f3c4a07ee0cb61ff79a79619"
+checksum = "b544ef1b4eac5dc2db33ea63606ae9ffcfac26c1416a2806ae0bf5f56b201191"
 dependencies = [
  "aho-corasick",
  "memchr",
- "regex-automata 0.4.7",
- "regex-syntax 0.8.4",
+ "regex-automata 0.4.9",
+ "regex-syntax 0.8.5",
 ]
 
 [[package]]
@@ -3958,13 +4060,13 @@ dependencies = [
 
 [[package]]
 name = "regex-automata"
-version = "0.4.7"
+version = "0.4.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df"
+checksum = "809e8dc61f6de73b46c85f4c96486310fe304c434cfa43669d7b40f711150908"
 dependencies = [
  "aho-corasick",
  "memchr",
- "regex-syntax 0.8.4",
+ "regex-syntax 0.8.5",
 ]
 
 [[package]]
@@ -3981,9 +4083,9 @@ checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1"
 
 [[package]]
 name = "regex-syntax"
-version = "0.8.4"
+version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b"
+checksum = "2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c"
 
 [[package]]
 name = "relative-path"
@@ -4002,9 +4104,9 @@ dependencies = [
 
 [[package]]
 name = "reqwest"
-version = "0.12.7"
+version = "0.12.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f8f4955649ef5c38cc7f9e8aa41761d48fb9677197daea9984dc54f56aad5e63"
+checksum = "a77c62af46e79de0a562e1a9849205ffcb7fc1238876e9bd743357570e04046f"
 dependencies = [
  "base64 0.22.1",
  "bytes",
@@ -4045,9 +4147,9 @@ dependencies = [
 
 [[package]]
 name = "rgb"
-version = "0.8.47"
+version = "0.8.50"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e12bc8d2f72df26a5d3178022df33720fbede0d31d82c7291662eff89836994d"
+checksum = "57397d16646700483b67d2dd6511d79318f9d057fdbd21a4066aeac8b41d310a"
 dependencies = [
  "bytemuck",
 ]
@@ -4069,9 +4171,9 @@ dependencies = [
 
 [[package]]
 name = "rkyv"
-version = "0.7.44"
+version = "0.7.45"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5cba464629b3394fc4dbc6f940ff8f5b4ff5c7aef40f29166fd4ad12acbc99c0"
+checksum = "9008cd6385b9e161d8229e1f6549dd23c3d022f132a2ea37ac3a10ac4935779b"
 dependencies = [
  "bitvec",
  "bytecheck",
@@ -4087,9 +4189,9 @@ dependencies = [
 
 [[package]]
 name = "rkyv_derive"
-version = "0.7.44"
+version = "0.7.45"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a7dddfff8de25e6f62b9d64e6e432bf1c6736c57d20323e15ee10435fbda7c65"
+checksum = "503d1d27590a2b0a3a4ca4c94755aa2875657196ecbf401a42eff41d7de532c0"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -4143,7 +4245,7 @@ dependencies = [
  "regex",
  "relative-path",
  "rustc_version 0.4.1",
- "syn 2.0.85",
+ "syn 2.0.87",
  "unicode-ident",
 ]
 
@@ -4181,7 +4283,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rust-embed-utils",
- "syn 2.0.85",
+ "syn 2.0.87",
  "walkdir",
 ]
 
@@ -4197,9 +4299,9 @@ dependencies = [
 
 [[package]]
 name = "rust_decimal"
-version = "1.35.0"
+version = "1.36.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1790d1c4c0ca81211399e0e0af16333276f375209e71a37b67698a373db5b47a"
+checksum = "b082d80e3e3cc52b2ed634388d436fe1f4de6af5786cc2de9ba9737527bdf555"
 dependencies = [
  "arrayvec",
  "borsh",
@@ -4249,9 +4351,9 @@ dependencies = [
 
 [[package]]
 name = "rustix"
-version = "0.38.37"
+version = "0.38.40"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8acb788b847c24f28525660c4d7758620a7210875711f79e7f663cc152726811"
+checksum = "99e4ea3e1cdc4b559b8e5650f9c8e5998e3e5c1343b4eaf034565f32318d63c0"
 dependencies = [
  "bitflags 2.6.0",
  "errno",
@@ -4262,9 +4364,9 @@ dependencies = [
 
 [[package]]
 name = "rustls"
-version = "0.23.12"
+version = "0.23.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c58f8c84392efc0a126acce10fa59ff7b3d2ac06ab451a33f2741989b806b044"
+checksum = "eee87ff5d9b36712a58574e12e9f0ea80f915a5b0ac518d322b24a465617925e"
 dependencies = [
  "once_cell",
  "ring",
@@ -4276,19 +4378,18 @@ dependencies = [
 
 [[package]]
 name = "rustls-pemfile"
-version = "2.1.3"
+version = "2.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "196fe16b00e106300d3e45ecfcb764fa292a535d7326a29a5875c579c7417425"
+checksum = "dce314e5fee3f39953d46bb63bb8a46d40c2f8fb7cc5a3b6cab2bde9721d6e50"
 dependencies = [
- "base64 0.22.1",
  "rustls-pki-types",
 ]
 
 [[package]]
 name = "rustls-pki-types"
-version = "1.8.0"
+version = "1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fc0a2ce646f8655401bb81e7927b812614bd5d91dbc968696be50603510fcaf0"
+checksum = "16f1201b3c9a7ee8039bcadc17b7e605e2945b27eee7631788c1bd2b0643674b"
 
 [[package]]
 name = "rustls-webpki"
@@ -4303,9 +4404,9 @@ dependencies = [
 
 [[package]]
 name = "rustversion"
-version = "1.0.17"
+version = "1.0.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "955d28af4278de8121b7ebeb796b6a45735dc01436d898801014aced2773a3d6"
+checksum = "0e819f2bc632f285be6d7cd36e25940d45b2391dd6d9b939e79de557f7014248"
 
 [[package]]
 name = "ryu"
@@ -4388,7 +4489,7 @@ checksum = "ad1e866f866923f252f05c889987993144fb74e722403468a4ebd70c3cd756c0"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -4451,7 +4552,7 @@ dependencies = [
  "darling",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -4528,9 +4629,9 @@ dependencies = [
 
 [[package]]
 name = "simdutf8"
-version = "0.1.4"
+version = "0.1.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a"
+checksum = "e3a9fe34e3e7a50316060351f37187a3f546bce95496156754b601a5fa71b76e"
 
 [[package]]
 name = "similar"
@@ -4631,7 +4732,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "structmeta-derive",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -4642,7 +4743,7 @@ checksum = "152a0b65a590ff6c3da95cabe2353ee04e6167c896b28e3b14478c2636c922fc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -4664,7 +4765,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -4675,9 +4776,9 @@ checksum = "13c2bddecc57b384dee18652358fb23172facb8a2c51ccc10d74c157bdea3292"
 
 [[package]]
 name = "symbolic-common"
-version = "12.10.0"
+version = "12.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "16629323a4ec5268ad23a575110a724ad4544aae623451de600c747bf87b36cf"
+checksum = "3d4d73159efebfb389d819fd479afb2dbd57dcb3e3f4b7fcfa0e675f5a46c1cb"
 dependencies = [
  "debugid",
  "memmap2",
@@ -4687,9 +4788,9 @@ dependencies = [
 
 [[package]]
 name = "symbolic-demangle"
-version = "12.10.0"
+version = "12.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "48c043a45f08f41187414592b3ceb53fb0687da57209cc77401767fb69d5b596"
+checksum = "a767859f6549c665011970874c3f541838b4835d5aaaa493d3ee383918be9f10"
 dependencies = [
  "cpp_demangle",
  "rustc-demangle",
@@ -4709,9 +4810,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.85"
+version = "2.0.87"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5023162dfcd14ef8f32034d8bcd4cc5ddc61ef7a247c024a33e24e1f24d21b56"
+checksum = "25aa4ce346d03a6dcd68dd8b4010bcb74e54e62c90c573f394c46eae99aba32d"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -4719,24 +4820,23 @@ dependencies = [
 ]
 
 [[package]]
-name = "syn_derive"
-version = "0.1.8"
+name = "sync_wrapper"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1329189c02ff984e9736652b1631330da25eaa6bc639089ed4915d25446cbe7b"
+checksum = "a7065abeca94b6a8a577f9bd45aa0867a2238b74e8eb67cf10d492bc39351394"
 dependencies = [
- "proc-macro-error",
- "proc-macro2",
- "quote",
- "syn 2.0.85",
+ "futures-core",
 ]
 
 [[package]]
-name = "sync_wrapper"
-version = "1.0.1"
+name = "synstructure"
+version = "0.13.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a7065abeca94b6a8a577f9bd45aa0867a2238b74e8eb67cf10d492bc39351394"
+checksum = "c8af7666ab7b6390ab78131fb5b0fce11d6b7a6951602017c35fa82800708971"
 dependencies = [
- "futures-core",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -4753,9 +4853,9 @@ checksum = "921f1e9c427802414907a48b21a6504ff6b3a15a1a3cf37e699590949ad9befc"
 
 [[package]]
 name = "tempfile"
-version = "3.13.0"
+version = "3.14.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f0f2c9fc62d0beef6951ccffd757e241266a2c833136efbe35af6cd2567dca5b"
+checksum = "28cce251fcbc87fac86a866eeb0d6c2d536fc16d06f184bb61aeae11aa4cee0c"
 dependencies = [
  "cfg-if",
  "fastrand",
@@ -4766,22 +4866,22 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.63"
+version = "1.0.69"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c0342370b38b6a11b6cc11d6a805569958d54cfa061a29969c3b5ce2ea405724"
+checksum = "b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.63"
+version = "1.0.69"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a4558b58466b9ad7ca0f102865eccc95938dca1a74a856f2b57b6629050da261"
+checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -4831,6 +4931,16 @@ dependencies = [
  "time-core",
 ]
 
+[[package]]
+name = "tinystr"
+version = "0.7.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9117f5d4db391c1cf6927e7bea3db74b9a1c1add8f7eda9ffd5364f40f57b82f"
+dependencies = [
+ "displaydoc",
+ "zerovec",
+]
+
 [[package]]
 name = "tinytemplate"
 version = "1.2.1"
@@ -4882,14 +4992,14 @@ checksum = "693d596312e88961bc67d7f1f97af8a70227d9f90c31bba5806eec004978d752"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
 name = "tokio-postgres"
-version = "0.7.11"
+version = "0.7.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "03adcf0147e203b6032c0b2d30be1415ba03bc348901f3ff1cc0df6a733e60c3"
+checksum = "3b5d3742945bc7d7f210693b0c58ae542c6fd47b17adbbda0885f3dcb34a6bdb"
 dependencies = [
  "async-trait",
  "byteorder",
@@ -4924,9 +5034,9 @@ dependencies = [
 
 [[package]]
 name = "tokio-util"
-version = "0.7.11"
+version = "0.7.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9cf6b47b3771c49ac75ad09a6162f53ad4b8088b76ac60e8ec1455b31a189fe1"
+checksum = "61e7c3654c13bcd040d4a03abee2c75b1d14a37b423cf5a813ceae1cc903ec6a"
 dependencies = [
  "bytes",
  "futures-core",
@@ -4969,27 +5079,6 @@ dependencies = [
  "winnow",
 ]
 
-[[package]]
-name = "tower"
-version = "0.4.13"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b8fa9be0de6cf49e536ce1851f987bd21a43b771b09473c3549a6c853db37c1c"
-dependencies = [
- "futures-core",
- "futures-util",
- "pin-project",
- "pin-project-lite",
- "tokio",
- "tower-layer",
- "tower-service",
-]
-
-[[package]]
-name = "tower-layer"
-version = "0.3.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "121c2a6cda46980bb0fcd1647ffaf6cd3fc79a013de288782836f6df9c48780e"
-
 [[package]]
 name = "tower-service"
 version = "0.3.3"
@@ -5016,7 +5105,7 @@ checksum = "34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -5076,7 +5165,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "04659ddb06c87d233c566112c1c9c5b9e98256d9af50ec3bc9c8327f873a7568"
 dependencies = [
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -5093,9 +5182,9 @@ checksum = "e421abadd41a4225275504ea4d6566923418b7f05506fbc9c0fe86ba7396114b"
 
 [[package]]
 name = "typeid"
-version = "1.0.0"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "059d83cc991e7a42fc37bd50941885db0888e34209f8cfd9aab07ddec03bc9cf"
+checksum = "0e13db2e0ccd5e14a544e8a246ba2312cd25223f616442d7f2cb0e3db614236e"
 
 [[package]]
 name = "typenum"
@@ -5105,18 +5194,15 @@ checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
 
 [[package]]
 name = "unicase"
-version = "2.7.0"
+version = "2.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f7d2d4dafb69621809a81864c9c1b864479e1235c0dd4e199924b9742439ed89"
-dependencies = [
- "version_check",
-]
+checksum = "7e51b68083f157f853b6379db119d1c1be0e6e4dec98101079dec41f6f5cf6df"
 
 [[package]]
 name = "unicode-bidi"
-version = "0.3.15"
+version = "0.3.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "08f95100a766bf4f8f28f90d77e0a5461bbdb219042e7679bebe79004fed8d75"
+checksum = "5ab17db44d7388991a428b2ee655ce0c212e862eff1768a455c58f9aad6e7893"
 
 [[package]]
 name = "unicode-ident"
@@ -5126,30 +5212,30 @@ checksum = "e91b56cd4cadaeb79bbf1a5645f6b4f8dc5bde8834ad5894a8db35fda9efa1fe"
 
 [[package]]
 name = "unicode-normalization"
-version = "0.1.23"
+version = "0.1.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a56d1686db2308d901306f92a263857ef59ea39678a5458e7cb17f01415101f5"
+checksum = "5033c97c4262335cded6d6fc3e5c18ab755e1a3dc96376350f3d8e9f009ad956"
 dependencies = [
  "tinyvec",
 ]
 
 [[package]]
 name = "unicode-properties"
-version = "0.1.1"
+version = "0.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e4259d9d4425d9f0661581b804cb85fe66a4c631cadd8f490d1c13a35d5d9291"
+checksum = "e70f2a8b45122e719eb623c01822704c4e0907e7e426a05927e1a1cfff5b75d0"
 
 [[package]]
 name = "unicode-segmentation"
-version = "1.11.0"
+version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d4c87d22b6e3f4a18d4d40ef354e97c90fcb14dd91d7dc0aa9d8a1172ebf7202"
+checksum = "f6ccf251212114b54433ec949fd6a7841275f9ada20dddd2f29e9ceea4501493"
 
 [[package]]
 name = "unicode-width"
-version = "0.1.13"
+version = "0.1.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d"
+checksum = "7dd6e30e90baa6f72411720665d41d89b9a3d039dc45b8faea1ddd07f617f6af"
 
 [[package]]
 name = "unsafe-libyaml"
@@ -5165,9 +5251,9 @@ checksum = "8ecb6da28b8a351d773b68d5825ac39017e680750f980f3a1a85cd8dd28a47c1"
 
 [[package]]
 name = "url"
-version = "2.5.2"
+version = "2.5.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "22784dbdf76fdde8af1aeda5622b546b422b6fc585325248a2bf9f5e41e94d6c"
+checksum = "8d157f1b96d14500ffdc1f10ba712e780825526c03d9a49b4d0324b0d9113ada"
 dependencies = [
  "form_urlencoded",
  "idna",
@@ -5180,12 +5266,24 @@ version = "2.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "daf8dba3b7eb870caf1ddeed7bc9d2a049f3cfdfae7cb521b087cc33ae4c49da"
 
+[[package]]
+name = "utf16_iter"
+version = "1.0.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c8232dd3cdaed5356e0f716d285e4b40b932ac434100fe9b7e0e8e935b9e6246"
+
 [[package]]
 name = "utf8-width"
 version = "0.1.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "86bd8d4e895da8537e5315b8254664e6b769c4ff3db18321b297a1e7004392e3"
 
+[[package]]
+name = "utf8_iter"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6c140620e7ffbb22c2dee59cafe6084a59b5ffc27a8859a5f0d494b5d52b6be"
+
 [[package]]
 name = "utf8parse"
 version = "0.2.2"
@@ -5202,7 +5300,7 @@ dependencies = [
  "serde",
  "serde_json",
  "serde_yaml",
- "utoipa-gen 4.3.0",
+ "utoipa-gen 4.3.1",
 ]
 
 [[package]]
@@ -5230,15 +5328,15 @@ dependencies = [
 
 [[package]]
 name = "utoipa-gen"
-version = "4.3.0"
+version = "4.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7bf0e16c02bc4bf5322ab65f10ab1149bdbcaa782cba66dc7057370a3f8190be"
+checksum = "20c24e8ab68ff9ee746aad22d39b5535601e6416d1b0feeabf78be986a5c4392"
 dependencies = [
  "proc-macro-error",
  "proc-macro2",
  "quote",
  "regex",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -5249,7 +5347,7 @@ checksum = "5629efe65599d0ccd5d493688cbf6e03aa7c1da07fe59ff97cf5977ed0637f66"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -5289,9 +5387,9 @@ checksum = "830b7e5d4d90034032940e4ace0d9a9a057e7a45cd94e6c007832e39edb82f6d"
 
 [[package]]
 name = "value-bag"
-version = "1.9.0"
+version = "1.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a84c137d37ab0142f0f2ddfe332651fdbf252e7b7dbb4e67b6c1f1b2e925101"
+checksum = "3ef4c4aa54d5d05a279399bfa921ec387b7aba77caf7a682ae8d86785b8fdad2"
 
 [[package]]
 name = "vcpkg"
@@ -5347,34 +5445,35 @@ checksum = "b8dad83b4f25e74f184f64c43b150b91efe7647395b42289f38e50566d82855b"
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.92"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4be2531df63900aeb2bca0daaaddec08491ee64ceecbee5076636a3b026795a8"
+checksum = "128d1e363af62632b8eb57219c8fd7877144af57558fb2ef0368d0087bddeb2e"
 dependencies = [
  "cfg-if",
+ "once_cell",
  "wasm-bindgen-macro",
 ]
 
 [[package]]
 name = "wasm-bindgen-backend"
-version = "0.2.92"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "614d787b966d3989fa7bb98a654e369c762374fd3213d212cfc0251257e747da"
+checksum = "cb6dd4d3ca0ddffd1dd1c9c04f94b868c37ff5fac97c30b97cff2d74fce3a358"
 dependencies = [
  "bumpalo",
  "log",
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-futures"
-version = "0.4.42"
+version = "0.4.45"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "76bc14366121efc8dbb487ab05bcc9d346b3b5ec0eaa76e46594cabbe51762c0"
+checksum = "cc7ec4f8827a71586374db3e87abdb5a2bb3a15afed140221307c3ec06b1f63b"
 dependencies = [
  "cfg-if",
  "js-sys",
@@ -5384,9 +5483,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.92"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1f8823de937b71b9460c0c34e25f3da88250760bec0ebac694b49997550d726"
+checksum = "e79384be7f8f5a9dd5d7167216f022090cf1f9ec128e6e6a482a2cb5c5422c56"
 dependencies = [
  "quote",
  "wasm-bindgen-macro-support",
@@ -5394,28 +5493,28 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.92"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7"
+checksum = "26c6ab57572f7a24a4985830b120de1594465e5d500f24afe89e16b4e833ef68"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.92"
+version = "0.2.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96"
+checksum = "65fc09f10666a9f147042251e0dda9c18f166ff7de300607007e96bdebc1068d"
 
 [[package]]
 name = "web-sys"
-version = "0.3.69"
+version = "0.3.72"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77afa9a11836342370f4817622a2f0f418b134426d91a82dfb48f532d2ec13ef"
+checksum = "f6488b90108c040df0fe62fa815cbdee25124641df01814dd7282749234c6112"
 dependencies = [
  "js-sys",
  "wasm-bindgen",
@@ -5433,29 +5532,29 @@ dependencies = [
 
 [[package]]
 name = "webpki-roots"
-version = "0.26.5"
+version = "0.26.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0bd24728e5af82c6c4ec1b66ac4844bdf8156257fccda846ec58b42cd0cdbe6a"
+checksum = "841c67bff177718f1d4dfefde8d8f0e78f9b6589319ba88312f567fc5841a958"
 dependencies = [
  "rustls-pki-types",
 ]
 
 [[package]]
 name = "whoami"
-version = "1.5.1"
+version = "1.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a44ab49fad634e88f55bf8f9bb3abd2f27d7204172a112c7c9987e01c1c94ea9"
+checksum = "372d5b87f58ec45c384ba03563b03544dc5fadc3983e434b286913f5b4a9bb6d"
 dependencies = [
- "redox_syscall 0.4.1",
+ "redox_syscall",
  "wasite",
  "web-sys",
 ]
 
 [[package]]
 name = "wide"
-version = "0.7.26"
+version = "0.7.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "901e8597c777fa042e9e245bd56c0dc4418c5db3f845b6ff94fbac732c6a0692"
+checksum = "b828f995bf1e9622031f8009f8481a85406ce1f4d4588ff746d872043e855690"
 dependencies = [
  "bytemuck",
  "safe_arch",
@@ -5622,6 +5721,18 @@ dependencies = [
  "memchr",
 ]
 
+[[package]]
+name = "write16"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d1890f4022759daae28ed4fe62859b1236caebfc61ede2f63ed4e695f3f6d936"
+
+[[package]]
+name = "writeable"
+version = "0.5.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e9df38ee2d2c3c5948ea468a8406ff0db0b29ae1ffde1bcf20ef305bcc95c51"
+
 [[package]]
 name = "wyz"
 version = "0.5.1"
@@ -5646,6 +5757,30 @@ version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "cfe53a6657fd280eaa890a3bc59152892ffa3e30101319d168b781ed6529b049"
 
+[[package]]
+name = "yoke"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6c5b1314b079b0930c31e3af543d8ee1757b1951ae1e1565ec704403a7240ca5"
+dependencies = [
+ "serde",
+ "stable_deref_trait",
+ "yoke-derive",
+ "zerofrom",
+]
+
+[[package]]
+name = "yoke-derive"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "28cc31741b18cb6f1d5ff12f5b7523e3d6eb0852bbbad19d73905511d9849b95"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.87",
+ "synstructure",
+]
+
 [[package]]
 name = "zerocopy"
 version = "0.7.35"
@@ -5664,7 +5799,28 @@ checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
+]
+
+[[package]]
+name = "zerofrom"
+version = "0.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "91ec111ce797d0e0784a1116d0ddcdbea84322cd79e5d5ad173daeba4f93ab55"
+dependencies = [
+ "zerofrom-derive",
+]
+
+[[package]]
+name = "zerofrom-derive"
+version = "0.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0ea7b4a3637ea8669cedf0f1fd5c286a17f3de97b8dd5a70a6c167a1730e63a5"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.87",
+ "synstructure",
 ]
 
 [[package]]
@@ -5673,6 +5829,28 @@ version = "1.8.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde"
 
+[[package]]
+name = "zerovec"
+version = "0.10.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "aa2b893d79df23bfb12d5461018d408ea19dfafe76c2c7ef6d4eba614f8ff079"
+dependencies = [
+ "yoke",
+ "zerofrom",
+ "zerovec-derive",
+]
+
+[[package]]
+name = "zerovec-derive"
+version = "0.10.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6eafa6dfb17584ea3e2bd6e76e0cc15ad7af12b09abdd1ca55961bed9b1063c6"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.87",
+]
+
 [[package]]
 name = "zip"
 version = "1.1.4"
diff --git a/src/annotate/seqvars/csq.rs b/src/annotate/seqvars/csq.rs
index 46ee1d30..1df50ded 100644
--- a/src/annotate/seqvars/csq.rs
+++ b/src/annotate/seqvars/csq.rs
@@ -1,9 +1,7 @@
 //! Compute molecular consequence of variants.
-use std::{collections::HashMap, sync::Arc};
-
-use crate::pbs::txs::{Strand, TranscriptBiotype, TranscriptTag};
+use crate::pbs::txs::{GenomeAlignment, Strand, TranscriptBiotype, TranscriptTag};
 use enumflags2::BitFlags;
-use hgvs::parser::NoRef;
+use hgvs::parser::{NoRef, ProteinEdit, UncertainLengthChange};
 use hgvs::{
     data::interface::{Provider, TxForRegionRecord},
     mapper::{assembly, Error},
@@ -12,6 +10,9 @@ use hgvs::{
     },
 };
 use itertools::Itertools;
+use std::cmp::Ordering;
+use std::ops::Range;
+use std::{collections::HashMap, sync::Arc};
 
 use super::{
     ann::{Allele, AnnField, Consequence, FeatureBiotype, FeatureType, Pos, Rank, SoFeature},
@@ -100,6 +101,8 @@ pub const PADDING: i32 = 5_000;
 /// Generally used alternative alignment method.
 pub const ALT_ALN_METHOD: &str = "splign";
 
+pub type Consequences = BitFlags<Consequence>;
+
 impl ConsequencePredictor {
     pub fn new(provider: Arc<MehariProvider>, config: Config) -> Self {
         tracing::info!("Building transcript interval trees ...");
@@ -374,7 +377,7 @@ impl ConsequencePredictor {
         let alignment = tx.genome_alignments.first().unwrap();
         let strand = Strand::try_from(alignment.strand).expect("invalid strand");
 
-        let mut consequences: BitFlags<Consequence> = BitFlags::empty();
+        let mut consequences = Consequences::empty();
 
         let mut min_start = None;
         let mut max_end = None;
@@ -389,14 +392,6 @@ impl ConsequencePredictor {
         let mut distance: Option<i32> = None;
         let mut tx_len = 0;
 
-        fn overlaps(
-            var_start: i32,
-            var_end: i32,
-            exon_intron_start: i32,
-            exon_intron_end: i32,
-        ) -> bool {
-            (var_start < exon_intron_end) && (var_end > exon_intron_start)
-        }
         let var_overlaps =
             |start: i32, end: i32| -> bool { overlaps(var_start, var_end, start, end) };
 
@@ -448,109 +443,22 @@ impl ConsequencePredictor {
                 }
             }
 
-            // Check the cases where the variant overlaps with whole exon.
-            if var_start <= exon_start && var_end >= exon_end {
-                consequences |= Consequence::ExonLossVariant;
-                if var_start < exon_start {
-                    if strand == Strand::Plus && !rank.is_first() {
-                        consequences |= Consequence::SpliceAcceptorVariant;
-                    } else if strand == Strand::Minus && !rank.is_last() {
-                        consequences |= Consequence::SpliceDonorVariant;
-                    }
-                }
-                if var_end > exon_end {
-                    if strand == Strand::Plus && !rank.is_last() {
-                        consequences |= Consequence::SpliceDonorVariant;
-                    } else if strand == Strand::Minus && !rank.is_last() {
-                        consequences |= Consequence::SpliceAcceptorVariant;
-                    }
-                }
-            }
-            if let Some(intron_start) = intron_start {
-                // For insertions, we need to consider the case of the insertion being right at
-                // the exon/intron junction.  We can express this with a shift of 1 for using
-                // "< / >" X +/- shift and meaning <= / >= X.
-                let ins_shift = if var.reference.is_empty() { 1 } else { 0 };
-
-                // Check the cases where the variant overlaps with the splice acceptor/donor site.
-                if var_overlaps(intron_start - ins_shift, intron_start + 2) {
-                    // Left side, is acceptor/donor depending on transcript's strand.
-                    match strand {
-                        Strand::Plus => consequences.insert(Consequence::SpliceDonorVariant),
-                        Strand::Minus => consequences.insert(Consequence::SpliceAcceptorVariant),
-                        _ => unreachable!("invalid strand: {}", alignment.strand),
-                    }
-                }
-                // Check the case where the variant overlaps with the splice donor site.
-                if var_overlaps(intron_end - 2, intron_end + ins_shift) {
-                    // Left side, is acceptor/donor depending on transcript's strand.
-                    match strand {
-                        Strand::Plus => consequences.insert(Consequence::SpliceAcceptorVariant),
-                        Strand::Minus => consequences.insert(Consequence::SpliceDonorVariant),
-                        _ => unreachable!("invalid strand: {}", alignment.strand),
-                    }
-                }
-            }
-            // Check the case where the variant overlaps with the splice region (1-3 bases in exon
-            // or 3-8 bases in intron).  We have to check all cases independently and not with `else`
-            // because the variant may be larger.
-            if let Some(intron_start) = intron_start {
-                if var_overlaps(intron_start + 2, intron_start + 8)
-                    || var_overlaps(intron_end - 8, intron_end - 2)
-                {
-                    consequences |= Consequence::SpliceRegionVariant;
-                }
-                if var_overlaps(exon_end - 3, exon_end) {
-                    if strand == Strand::Plus {
-                        if !rank.is_last() {
-                            consequences |= Consequence::SpliceRegionVariant;
-                        }
-                    } else {
-                        // alignment.strand == Strand::Minus
-                        if !rank.is_first() {
-                            consequences |= Consequence::SpliceRegionVariant;
-                        }
-                    }
-                }
-                if var_overlaps(exon_start, exon_start + 3) {
-                    if strand == Strand::Plus {
-                        if !rank.is_first() {
-                            consequences |= Consequence::SpliceRegionVariant;
-                        }
-                    } else {
-                        // alignment.strand == Strand::Minus
-                        if !rank.is_last() {
-                            consequences |= Consequence::SpliceRegionVariant;
-                        }
-                    }
-                }
-            }
+            let consequences_exonic = Self::analyze_exonic_variant(
+                var, strand, var_start, var_end, exon_start, exon_end, &rank,
+            );
+            consequences |= consequences_exonic;
 
             if let Some(intron_start) = intron_start {
-                // Check the case where the variant overlaps with the polypyrimidine tract.
-                // (A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17))
-                if strand == Strand::Plus && var_overlaps(intron_end - 17, intron_end - 2) {
-                    consequences |= Consequence::SplicePolypyrimidineTractVariant;
-                }
-                if strand == Strand::Minus && var_overlaps(intron_start + 2, intron_start + 17) {
-                    consequences |= Consequence::SplicePolypyrimidineTractVariant;
-                }
-                // Check conditions for splice_donor_region_variant
-                // (A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron))
-                if strand == Strand::Plus && var_overlaps(intron_start + 2, intron_start + 6) {
-                    consequences |= Consequence::SpliceDonorRegionVariant;
-                }
-                if strand == Strand::Minus && var_overlaps(intron_end - 6, intron_end - 2) {
-                    consequences |= Consequence::SpliceDonorRegionVariant;
-                }
-                // Check conditions for splice_donor_5th_base_variant
-                // (A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.)
-                if strand == Strand::Plus && var_overlaps(intron_start + 4, intron_start + 5) {
-                    consequences |= Consequence::SpliceDonorFifthBaseVariant;
-                }
-                if strand == Strand::Minus && var_overlaps(intron_end - 5, intron_end - 4) {
-                    consequences |= Consequence::SpliceDonorFifthBaseVariant;
-                }
+                let consequences_intronic = Self::analyze_intronic_variant(
+                    var,
+                    alignment,
+                    strand,
+                    var_start,
+                    var_end,
+                    intron_start,
+                    intron_end,
+                );
+                consequences |= consequences_intronic;
             }
 
             min_start = Some(std::cmp::min(min_start.unwrap_or(exon_start), exon_start));
@@ -697,153 +605,26 @@ impl ConsequencePredictor {
                         _ => panic!("Not a protein position: {:?}", &var_n),
                     };
 
-                    let conservative = match &var_c {
-                        HgvsVariant::CdsVariant { loc_edit, .. } => {
-                            // Handle the cases where the variant touches the start or stop codon based on `var_c`
-                            // coordinates.  The cases where the start/stop codon is touched by the variant
-                            // directly is handled above based on the `var_p` prediction.
-                            let loc = loc_edit.loc.inner();
-                            let start_base = loc.start.base;
-                            let start_cds_from = loc.start.cds_from;
-                            let end_base = loc.end.base;
-                            let end_cds_from = loc.end.cds_from;
-                            // The variables below mean "VARIANT_{starts,stops}_{left,right}_OF_{start,stop}_CODON".
-                            //
-                            // start codon
-                            let starts_left_of_start =
-                                start_cds_from == CdsFrom::Start && start_base < 0;
-                            let ends_right_of_start =
-                                start_cds_from != CdsFrom::Start || start_base > 0;
-                            if starts_left_of_start && ends_right_of_start {
-                                consequences |= Consequence::StartLost;
-                            }
-                            // stop codon
-                            let starts_left_of_stop = start_cds_from == CdsFrom::Start;
-                            let ends_right_of_stop = end_cds_from == CdsFrom::End;
-                            if starts_left_of_stop && ends_right_of_stop {
-                                consequences |= Consequence::StopLost;
-                            }
-
-                            // Detect variants affecting the 5'/3' UTRs.
-                            if start_cds_from == CdsFrom::Start {
-                                if start_base < 0 {
-                                    if is_intronic {
-                                        consequences |= Consequence::FivePrimeUtrIntronVariant;
-                                    }
-                                    if is_exonic {
-                                        consequences |= Consequence::FivePrimeUtrExonVariant;
-                                    }
-                                }
-                            } else if end_cds_from == CdsFrom::End {
-                                if is_intronic {
-                                    consequences |= Consequence::ThreePrimeUtrIntronVariant;
-                                }
-                                if is_exonic {
-                                    consequences |= Consequence::ThreePrimeUtrExonVariant;
-                                }
-                            }
-
-                            // The range is "conservative" (regarding deletions and insertions) if
-                            // it does not start or end within exons.
-                            start_cds_from == CdsFrom::Start
-                                && end_cds_from == CdsFrom::Start
-                                && start_base % 3 == 1
-                                && (end_base + 1) % 3 == 1
-                        }
-                        _ => panic!("Must be CDS variant: {}", &var_c),
-                    };
+                    let conservative = is_conservative_cds_variant(&var_c);
 
-                    fn is_stop(s: &str) -> bool {
-                        s == "X" || s == "Ter" || s == "*"
-                    }
+                    let consequences_cds =
+                        Self::analyze_cds_variant(&var_c, is_exonic, is_intronic, conservative);
 
                     // Analyze `var_p` for changes in the protein sequence.
-                    match &var_p {
-                        HgvsVariant::ProtVariant { loc_edit, .. } => match loc_edit {
-                            ProtLocEdit::Ordinary { loc, edit } => {
-                                let loc = loc.inner();
-                                match edit.inner() {
-                                    hgvs::parser::ProteinEdit::Fs { .. } => {
-                                        consequences |= Consequence::FrameshiftVariant;
-                                    }
-                                    hgvs::parser::ProteinEdit::Ext { .. } => {
-                                        consequences |= Consequence::StopLost;
-                                        consequences |= Consequence::FeatureElongation;
-                                    }
-                                    hgvs::parser::ProteinEdit::Subst { alternative } => {
-                                        if alternative.is_empty() {
-                                            consequences |= Consequence::SynonymousVariant;
-                                        } else if is_stop(alternative) {
-                                            if loc.start == loc.end && is_stop(&loc.start.aa) {
-                                                consequences |= Consequence::StopRetainedVariant;
-                                            } else {
-                                                consequences |= Consequence::StopGained;
-                                                // if the substitution happens right before the stop codon
-                                                // and if it is a conservative change
-                                                // then it is not a stop gained
-                                                // cf. 1:43450470:GCCT:G, ENST00000634258.3:c.10294_10296del/p.Leu3432Ter
-                                                if let Some(ref p) = protein_pos {
-                                                    if p.total.is_some_and(|t| p.ord == t - 1)
-                                                        && conservative
-                                                    {
-                                                        consequences &= !Consequence::StopGained;
-                                                        consequences |= Consequence::ConservativeInframeDeletion;
-                                                    }
-                                                }
-                                            }
-                                        } else {
-                                            consequences |= Consequence::MissenseVariant;
-                                        }
-                                    }
-                                    hgvs::parser::ProteinEdit::DelIns { alternative } => {
-                                        if conservative {
-                                            consequences |=
-                                                Consequence::ConservativeInframeDeletion;
-                                        } else {
-                                            consequences |= Consequence::DisruptiveInframeDeletion;
-                                        }
-                                        if alternative.contains('*')
-                                            || alternative.contains('X')
-                                            || alternative.contains("Ter")
-                                        {
-                                            consequences |= Consequence::StopGained;
-                                        }
-                                    }
-                                    hgvs::parser::ProteinEdit::Ins { .. }
-                                    | hgvs::parser::ProteinEdit::Dup => {
-                                        if conservative {
-                                            consequences |=
-                                                Consequence::ConservativeInframeInsertion;
-                                        } else {
-                                            consequences |= Consequence::DisruptiveInframeInsertion;
-                                        }
-                                        consequences |= Consequence::ConservativeInframeInsertion;
-                                    }
-                                    hgvs::parser::ProteinEdit::Del => {
-                                        if conservative {
-                                            consequences |=
-                                                Consequence::ConservativeInframeDeletion;
-                                        } else {
-                                            consequences |= Consequence::DisruptiveInframeDeletion;
-                                        }
-                                    }
-                                    hgvs::parser::ProteinEdit::Ident => {
-                                        consequences |= Consequence::SynonymousVariant;
-                                    }
-                                };
-                            }
-                            ProtLocEdit::NoChange | ProtLocEdit::NoChangeUncertain => {
-                                consequences |= Consequence::SynonymousVariant;
-                            }
-                            ProtLocEdit::InitiationUncertain => {
-                                consequences |= Consequence::StartLost;
-                            }
-                            ProtLocEdit::NoProtein
-                            | ProtLocEdit::NoProteinUncertain
-                            | ProtLocEdit::Unknown => (),
-                        },
-                        _ => panic!("Must be protein variant: {}", &var_p),
-                    }
+                    let consequences_protein =
+                        Self::analyze_protein_variant(&var_p, &protein_pos, conservative);
+
+                    consequences |= consequences_cds | consequences_protein;
+
+                    self.consequences_fix_special_cases(
+                        &mut consequences,
+                        consequences_cds,
+                        consequences_protein,
+                        &var_g,
+                        &var_n,
+                        &var_c,
+                        &var_p,
+                    );
 
                     (var_c, Some(var_p), hgvs_p, cds_pos, protein_pos)
                 }
@@ -915,6 +696,445 @@ impl ConsequencePredictor {
         }))
     }
 
+    #[allow(clippy::too_many_arguments, unused_variables)]
+    fn consequences_fix_special_cases(
+        &self,
+        consequences: &mut Consequences,
+        consequences_cds: Consequences,
+        consequences_protein: Consequences,
+        var_g: &HgvsVariant,
+        var_n: &HgvsVariant,
+        var_c: &HgvsVariant,
+        var_p: &HgvsVariant,
+    ) {
+        fn is_stop(s: &str) -> bool {
+            s == "X" || s == "Ter" || s == "*"
+        }
+
+        // In some cases, we predict a stop lost based on the cds variant
+        // but the protein translation does not confirm this.
+        //
+        // e.g.:
+        // 20:35511609:CAAGCCGCCTCCAGGTAGCAGCCACAGCCAGGAGCACACAGACAGAAGACTGTGTCATGGGTCATGGCCCCTCCGCACACCTACAGGTTTGCCAAAGGAA:C
+        if consequences_cds.contains(Consequence::StopLost)
+            && !consequences_protein.contains(Consequence::StopLost)
+        {
+            if let HgvsVariant::ProtVariant {
+                loc_edit: ProtLocEdit::Ordinary { loc, edit },
+                ..
+            } = var_p
+            {
+                match edit.inner() {
+                    // Stop lost due to a deletion in the CDS, but the resulting protein translation
+                    // continues to have a stop codon at the same position.
+                    ProteinEdit::DelIns { alternative } => {
+                        let loc_length = Range::<i32>::from(loc.inner().clone()).len();
+                        match alternative.len().cmp(&loc_length) {
+                            Ordering::Equal => {
+                                *consequences &= !Consequence::StopLost;
+                                *consequences |= Consequence::StopRetainedVariant;
+                            }
+                            Ordering::Greater => {
+                                *consequences |= Consequence::FeatureElongation;
+                            }
+                            _ => {}
+                        }
+                    }
+                    // Detect cases where the frameshift resolves into
+                    // a missense + stop retained variant.
+                    // This is the shortest possible frameshift in hgvsp (fs*2).
+                    ProteinEdit::Fs {
+                        alternative,
+                        terminal,
+                        length,
+                    } => {
+                        if let (Some(alt), Some(terminal), UncertainLengthChange::Known(2)) =
+                            (alternative, terminal, length)
+                        {
+                            if is_stop(terminal) && alt.len() == 1 {
+                                *consequences |= Consequence::MissenseVariant;
+                                *consequences |= Consequence::StopRetainedVariant;
+                                *consequences &= !Consequence::StopLost;
+                                *consequences &= !Consequence::FrameshiftVariant;
+                            }
+                        }
+                    }
+                    _ => {}
+                }
+            }
+        }
+
+        // Similarly, for the start lost case
+        //
+        // e.g.:
+        // 13:32316456:TA:T
+        // (This case just shortens a poly-A from which the start codon starts)
+        if consequences_cds.contains(Consequence::StartLost)
+            && !consequences_protein.contains(Consequence::StartLost)
+        {
+            *consequences &= !Consequence::StartLost;
+        }
+        if consequences.contains(Consequence::StartLost) {
+            if let (
+                HgvsVariant::TxVariant {
+                    loc_edit: n_loc_edit,
+                    accession,
+                    ..
+                },
+                HgvsVariant::CdsVariant {
+                    loc_edit: c_loc_edit,
+                    ..
+                },
+            ) = (var_n, var_c)
+            {
+                let n_loc = n_loc_edit.loc.inner();
+                let c_edit = c_loc_edit.edit.inner();
+                let c_loc = c_loc_edit.loc.inner();
+
+                // If edit occurs within the first 3 bases of the CDS,
+                let (start, end) = (c_loc.start.base, c_loc.end.base);
+                if start >= 1
+                    && end <= 3
+                    && c_loc.start.cds_from == CdsFrom::Start
+                    && c_loc.end.cds_from == CdsFrom::Start
+                {
+                    // … then we need to check whether this is a start lost or a start retained.
+                    // To that end, extract the first 3 bases plus/minus 3 bases …
+                    if let Ok(first_codon_pm1) = self.provider.get_seq_part(
+                        &accession.value,
+                        Some(
+                            usize::try_from(n_loc.start.base - start + 1)
+                                .unwrap()
+                                .saturating_sub(4),
+                        ),
+                        Some(usize::try_from(n_loc.end.base - start + 1).unwrap() + 5),
+                    ) {
+                        // … and introduce the change into the sequence.
+                        let mut first_codon = first_codon_pm1.clone();
+                        let (start, end) = (start as usize, end as usize);
+                        let start_retained = match c_edit {
+                            NaEdit::DelRef { .. } => {
+                                first_codon.replace_range(3 + start - 1..=3 + end - 1, "");
+                                // If the first codon is still a start codon, then it is a start retained.
+                                first_codon[2..5].contains("ATG")
+                            }
+                            // TODO: handle other cases
+                            _ => false,
+                        };
+                        if start_retained {
+                            *consequences &= !Consequence::StartLost;
+                            *consequences |= Consequence::StartRetainedVariant;
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    #[allow(clippy::too_many_arguments, unused_variables)]
+    fn analyze_exonic_variant(
+        var: &VcfVariant,
+        strand: Strand,
+        var_start: i32,
+        var_end: i32,
+        exon_start: i32,
+        exon_end: i32,
+        rank: &Rank,
+    ) -> Consequences {
+        let mut consequences: Consequences = Consequences::empty();
+
+        let var_overlaps =
+            |start: i32, end: i32| -> bool { overlaps(var_start, var_end, start, end) };
+
+        // Check the cases where the variant overlaps with whole exon.
+        if var_start <= exon_start && var_end >= exon_end {
+            consequences |= Consequence::ExonLossVariant;
+            if var_start < exon_start {
+                if strand == Strand::Plus && !rank.is_first() {
+                    consequences |= Consequence::SpliceAcceptorVariant;
+                } else if strand == Strand::Minus && !rank.is_last() {
+                    consequences |= Consequence::SpliceDonorVariant;
+                }
+            }
+            if var_end > exon_end {
+                if strand == Strand::Plus && !rank.is_last() {
+                    consequences |= Consequence::SpliceDonorVariant;
+                } else if strand == Strand::Minus && !rank.is_last() {
+                    consequences |= Consequence::SpliceAcceptorVariant;
+                }
+            }
+        }
+
+        // Check splice region variants
+        if var_overlaps(exon_end - 3, exon_end) {
+            if strand == Strand::Plus {
+                if !rank.is_last() {
+                    consequences |= Consequence::SpliceRegionVariant;
+                }
+            } else {
+                // alignment.strand == Strand::Minus
+                if !rank.is_first() {
+                    consequences |= Consequence::SpliceRegionVariant;
+                }
+            }
+        }
+        if var_overlaps(exon_start, exon_start + 3) {
+            if strand == Strand::Plus {
+                if !rank.is_first() {
+                    consequences |= Consequence::SpliceRegionVariant;
+                }
+            } else {
+                // alignment.strand == Strand::Minus
+                if !rank.is_last() {
+                    consequences |= Consequence::SpliceRegionVariant;
+                }
+            }
+        }
+        consequences
+    }
+
+    #[allow(clippy::too_many_arguments)]
+    fn analyze_intronic_variant(
+        var: &VcfVariant,
+        alignment: &GenomeAlignment,
+        strand: Strand,
+        var_start: i32,
+        var_end: i32,
+        intron_start: i32,
+        intron_end: i32,
+    ) -> Consequences {
+        let mut consequences: Consequences = Consequences::empty();
+
+        let var_overlaps =
+            |start: i32, end: i32| -> bool { overlaps(var_start, var_end, start, end) };
+
+        // For insertions, we need to consider the case of the insertion being right at
+        // the exon/intron junction.  We can express this with a shift of 1 for using
+        // "< / >" X +/- shift and meaning <= / >= X.
+        let ins_shift = if var.reference.is_empty() { 1 } else { 0 };
+
+        // Check the cases where the variant overlaps with the splice acceptor/donor site.
+        if var_overlaps(intron_start - ins_shift, intron_start + 2) {
+            // Left side, is acceptor/donor depending on transcript's strand.
+            match strand {
+                Strand::Plus => {
+                    consequences |= Consequence::SpliceDonorVariant;
+                }
+                Strand::Minus => {
+                    consequences |= Consequence::SpliceAcceptorVariant;
+                }
+                _ => unreachable!("invalid strand: {}", alignment.strand),
+            }
+        }
+
+        // Check the case where the variant overlaps with the splice donor site.
+        if var_overlaps(intron_end - 2, intron_end + ins_shift) {
+            // Left side, is acceptor/donor depending on transcript's strand.
+            match strand {
+                Strand::Plus => {
+                    consequences |= Consequence::SpliceAcceptorVariant;
+                }
+                Strand::Minus => {
+                    consequences |= Consequence::SpliceDonorVariant;
+                }
+                _ => unreachable!("invalid strand: {}", alignment.strand),
+            }
+        }
+
+        // Check the case where the variant overlaps with the splice region (1-3 bases in exon
+        // or 3-8 bases in intron).
+        // We have to check all cases independently and not with `else`
+        // because the variant may be larger.
+        if var_overlaps(intron_start + 2, intron_start + 8)
+            || var_overlaps(intron_end - 8, intron_end - 2)
+        {
+            consequences |= Consequence::SpliceRegionVariant;
+        }
+
+        // Check the case where the variant overlaps with the polypyrimidine tract.
+        // (A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17))
+        if strand == Strand::Plus && var_overlaps(intron_end - 17, intron_end - 2) {
+            consequences |= Consequence::SplicePolypyrimidineTractVariant;
+        }
+        if strand == Strand::Minus && var_overlaps(intron_start + 2, intron_start + 17) {
+            consequences |= Consequence::SplicePolypyrimidineTractVariant;
+        }
+
+        // Check conditions for splice_donor_region_variant
+        // (A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron))
+        if strand == Strand::Plus && var_overlaps(intron_start + 2, intron_start + 6) {
+            consequences |= Consequence::SpliceDonorRegionVariant;
+        }
+        if strand == Strand::Minus && var_overlaps(intron_end - 6, intron_end - 2) {
+            consequences |= Consequence::SpliceDonorRegionVariant;
+        }
+
+        // Check conditions for splice_donor_5th_base_variant
+        // (A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.)
+        if strand == Strand::Plus && var_overlaps(intron_start + 4, intron_start + 5) {
+            consequences |= Consequence::SpliceDonorFifthBaseVariant;
+        }
+        if strand == Strand::Minus && var_overlaps(intron_end - 5, intron_end - 4) {
+            consequences |= Consequence::SpliceDonorFifthBaseVariant;
+        }
+
+        consequences
+    }
+
+    fn analyze_cds_variant(
+        var_c: &HgvsVariant,
+        is_exonic: bool,
+        is_intronic: bool,
+        _conservative: bool,
+    ) -> Consequences {
+        let mut consequences: Consequences = Consequences::empty();
+
+        if let HgvsVariant::CdsVariant { loc_edit, .. } = &var_c {
+            // Handle the cases where the variant touches the start or stop codon based on `var_c`
+            // coordinates.  The cases where the start/stop codon is touched by the variant
+            // directly is handled above based on the `var_p` prediction.
+            let loc = loc_edit.loc.inner();
+            let _edit = loc_edit.edit.inner();
+            let start_base = loc.start.base;
+            let start_cds_from = loc.start.cds_from;
+            // let end_base = loc.end.base;
+            let end_cds_from = loc.end.cds_from;
+
+            // The variables below mean "VARIANT_{starts,stops}_{left,right}_OF_{start,stop}_CODON".
+            //
+            // start codon
+            let starts_left_of_start = start_cds_from == CdsFrom::Start && start_base < 0;
+            let ends_right_of_start = start_cds_from != CdsFrom::Start || start_base > 0;
+            if starts_left_of_start && ends_right_of_start {
+                consequences |= Consequence::StartLost;
+            }
+            // stop codon
+            let starts_left_of_stop = start_cds_from == CdsFrom::Start;
+            let ends_right_of_stop = end_cds_from == CdsFrom::End;
+            if starts_left_of_stop && ends_right_of_stop {
+                consequences |= Consequence::StopLost;
+            }
+
+            // Detect variants affecting the 5'/3' UTRs.
+            if start_cds_from == CdsFrom::Start {
+                if start_base < 0 {
+                    if is_intronic {
+                        consequences |= Consequence::FivePrimeUtrIntronVariant;
+                    }
+                    if is_exonic {
+                        consequences |= Consequence::FivePrimeUtrExonVariant;
+                    }
+                }
+            } else if end_cds_from == CdsFrom::End {
+                if is_intronic {
+                    consequences |= Consequence::ThreePrimeUtrIntronVariant;
+                }
+                if is_exonic {
+                    consequences |= Consequence::ThreePrimeUtrExonVariant;
+                }
+            }
+        } else {
+            panic!("Must be CDS variant: {}", &var_c)
+        };
+        consequences
+    }
+
+    fn analyze_protein_variant(
+        var_p: &HgvsVariant,
+        protein_pos: &Option<Pos>,
+        conservative: bool,
+    ) -> Consequences {
+        let mut consequences: Consequences = Consequences::empty();
+
+        // TODO move to hgvs-rs library as method of `ProtPos` or similar
+        fn is_stop(s: &str) -> bool {
+            s == "X" || s == "Ter" || s == "*"
+        }
+
+        fn has_stop(s: &str) -> bool {
+            s.contains('*') || s.contains('X') || s.contains("Ter")
+        }
+
+        match var_p {
+            HgvsVariant::ProtVariant { loc_edit, .. } => match loc_edit {
+                ProtLocEdit::Ordinary { loc, edit } => {
+                    let loc = loc.inner();
+                    match edit.inner() {
+                        ProteinEdit::Fs { .. } => {
+                            consequences |= Consequence::FrameshiftVariant;
+                        }
+                        ProteinEdit::Ext { .. } => {
+                            consequences |= Consequence::StopLost;
+                            consequences |= Consequence::FeatureElongation;
+                        }
+                        ProteinEdit::Subst { alternative } => {
+                            if alternative.is_empty() {
+                                consequences |= Consequence::SynonymousVariant;
+                            } else if is_stop(alternative) {
+                                if loc.start == loc.end && is_stop(&loc.start.aa) {
+                                    consequences |= Consequence::StopRetainedVariant;
+                                } else {
+                                    consequences |= Consequence::StopGained;
+                                    // if the substitution happens right before the stop codon
+                                    // and if it is a conservative change
+                                    // then it is not a stop gained
+                                    // cf. 1:43450470:GCCT:G, ENST00000634258.3:c.10294_10296del/p.Leu3432Ter
+                                    if let Some(ref p) = protein_pos {
+                                        if p.total.is_some_and(|t| p.ord == t - 1) && conservative {
+                                            consequences &= !Consequence::StopGained;
+                                            consequences |=
+                                                Consequence::ConservativeInframeDeletion;
+                                        }
+                                    }
+                                }
+                            } else {
+                                consequences |= Consequence::MissenseVariant;
+                            }
+                        }
+                        ProteinEdit::DelIns { alternative } => {
+                            if conservative {
+                                consequences |= Consequence::ConservativeInframeDeletion;
+                            } else {
+                                consequences |= Consequence::DisruptiveInframeDeletion;
+                            }
+
+                            if has_stop(alternative) {
+                                consequences |= Consequence::StopGained;
+                            }
+                        }
+                        ProteinEdit::Ins { .. } | ProteinEdit::Dup => {
+                            if conservative {
+                                consequences |= Consequence::ConservativeInframeInsertion;
+                            } else {
+                                consequences |= Consequence::DisruptiveInframeInsertion;
+                            }
+                        }
+                        ProteinEdit::Del => {
+                            if conservative {
+                                consequences |= Consequence::ConservativeInframeDeletion;
+                            } else {
+                                consequences |= Consequence::DisruptiveInframeDeletion;
+                            }
+                        }
+                        ProteinEdit::Ident => {
+                            consequences |= Consequence::SynonymousVariant;
+                        }
+                    };
+                }
+                ProtLocEdit::NoChange | ProtLocEdit::NoChangeUncertain => {
+                    consequences |= Consequence::SynonymousVariant;
+                }
+                ProtLocEdit::InitiationUncertain => {
+                    consequences |= Consequence::StartLost;
+                }
+                ProtLocEdit::NoProtein | ProtLocEdit::NoProteinUncertain | ProtLocEdit::Unknown => {
+                }
+            },
+            _ => panic!("Must be protein variant: {}", &var_p),
+        }
+        consequences
+    }
+
     fn get_var_g(var: &VcfVariant, chrom_acc: &str) -> HgvsVariant {
         let chrom_acc = chrom_acc.to_string();
         HgvsVariant::GenomeVariant {
@@ -991,6 +1211,32 @@ impl ConsequencePredictor {
     }
 }
 
+fn is_conservative_cds_variant(var_c: &HgvsVariant) -> bool {
+    match var_c {
+        HgvsVariant::CdsVariant { loc_edit, .. } => {
+            // Handle the cases where the variant touches the start or stop codon based on `var_c`
+            // coordinates. The cases where the start/stop codon is touched by the variant
+            // directly is handled elsewhere based on the `var_p` prediction.
+            let loc = loc_edit.loc.inner();
+            let start_base = loc.start.base;
+            let start_cds_from = loc.start.cds_from;
+            let end_base = loc.end.base;
+            let end_cds_from = loc.end.cds_from;
+            // The range is "conservative" (regarding deletions and insertions) if
+            // it does not start or end within codons.
+            start_cds_from == CdsFrom::Start
+                && end_cds_from == CdsFrom::Start
+                && start_base % 3 == 1
+                && (end_base + 1) % 3 == 1
+        }
+        _ => panic!("Expected CdsVariant, got {:#?}", var_c),
+    }
+}
+
+fn overlaps(var_start: i32, var_end: i32, exon_intron_start: i32, exon_intron_end: i32) -> bool {
+    (var_start < exon_intron_end) && (var_end > exon_intron_start)
+}
+
 impl ConsequencePredictor {
     /// Return data version string (if set).
     pub fn data_version(&self) -> Option<String> {
@@ -1000,16 +1246,20 @@ impl ConsequencePredictor {
 
 #[cfg(test)]
 mod test {
-    use std::{fs::File, io::BufReader};
-
+    use super::*;
+    use crate::annotate::seqvars::provider::ConfigBuilder as MehariProviderConfigBuilder;
+    use crate::annotate::seqvars::{
+        load_tx_db, run_with_writer, Args, AsyncAnnotatedVariantWriter, PathOutput,
+        TranscriptPickType,
+    };
+    use crate::common::noodles::{open_variant_reader, open_variant_writer, NoodlesVariantReader};
     use csv::ReaderBuilder;
+    use futures::TryStreamExt;
     use pretty_assertions::assert_eq;
     use serde::Deserialize;
-
-    use crate::annotate::seqvars::provider::ConfigBuilder as MehariProviderConfigBuilder;
-    use crate::annotate::seqvars::{load_tx_db, TranscriptPickType};
-
-    use super::*;
+    use std::path::Path;
+    use std::{fs::File, io::BufReader};
+    use tempfile::NamedTempFile;
 
     #[test]
     fn test_sync() {
@@ -1456,6 +1706,65 @@ mod test {
         Ok(())
     }
 
+    /// This is a set of variants where VEP and mehari to disagree,
+    /// i.e. interesting/edge cases that are not as clear-cut as others.
+    ///
+    /// This test ensures we do not regress on these cases.
+    #[tokio::test]
+    async fn annotate_vep_disagreement_cases() -> Result<(), anyhow::Error> {
+        let tx_path =
+            "tests/data/annotate/db/grch38/GRCh38-ensembl.disagreement-subset.txs.bin.zst";
+
+        let path_input_vcf = "tests/data/annotate/seqvars/vep.disagreement-cases.vcf";
+        let expected_vcf = "tests/data/annotate/seqvars/vep.disagreement-cases.expected.vcf";
+        let output = NamedTempFile::new()?;
+        let mut writer = open_variant_writer(output.as_ref()).await?;
+        run_with_writer(
+            &mut writer,
+            &Args {
+                genome_release: None,
+                path_input_ped: None,
+                path_input_vcf: path_input_vcf.into(),
+                output: PathOutput {
+                    path_output_vcf: Some(output.as_ref().to_str().unwrap().into()),
+                    path_output_tsv: None,
+                },
+                transcript_source: Default::default(),
+                report_most_severe_consequence_by: Some(ConsequenceBy::Allele),
+                pick_transcript: vec![TranscriptPickType::ManeSelect],
+                pick_transcript_mode: Default::default(),
+                max_var_count: None,
+                hgnc: None,
+                sources: crate::annotate::seqvars::Sources {
+                    transcripts: Some(vec![tx_path.into()]),
+                    frequencies: None,
+                    clinvar: None,
+                },
+            },
+        )
+        .await?;
+        writer.shutdown().await?;
+
+        let records_written = read_vcf(output).await?;
+        let records_expected = read_vcf(expected_vcf).await?;
+        assert_eq!(records_written, records_expected);
+
+        Ok(())
+    }
+
+    async fn read_vcf(
+        path: impl AsRef<Path>,
+    ) -> Result<Vec<noodles::vcf::variant::RecordBuf>, anyhow::Error> {
+        let mut output_reader = open_variant_reader(path.as_ref()).await?;
+        let header = output_reader.read_header().await?;
+        let mut record_iter = output_reader.records(&header).await;
+        let mut records = Vec::new();
+        while let Some(record) = record_iter.try_next().await? {
+            records.push(record);
+        }
+        Ok(records)
+    }
+
     #[derive(Debug, Deserialize)]
     struct Record {
         pub var: String,
@@ -1603,117 +1912,111 @@ mod test {
                 for ann in anns.iter().filter(|ann| ann.feature_id == record.tx) {
                     // We perform a comparison based on strings because we may not be able to parse out
                     // all consequences from the other tool.
-                    let record_csqs = record
-                        .csq
-                        .split('&')
-                        .map(|s| s.to_string())
-                        .collect::<Vec<_>>();
+                    let record_csqs = record.csq.split('&').collect::<Vec<_>>();
 
                     let highest_impact = ann.consequences.first().unwrap().impact();
-                    let mut expected_one_of = ann
+                    let expected_one_of = ann
                         .consequences
                         .iter()
                         .filter(|csq| csq.impact() == highest_impact)
                         .map(|csq| csq.to_string())
                         .collect::<Vec<_>>();
+                    let mut expected_one_of = expected_one_of
+                        .iter()
+                        .map(|s| s.as_str())
+                        .collect::<Vec<_>>();
 
                     // Map effects a bit for VEP.
-                    if path_tsv.ends_with(".vep.tsv")
-                        && (expected_one_of.contains(&String::from("disruptive_inframe_deletion"))
-                            || expected_one_of
-                                .contains(&String::from("conservative_inframe_deletion")))
+                    if path_tsv.contains(".vep")
+                        && (expected_one_of.contains(&"disruptive_inframe_deletion")
+                            || expected_one_of.contains(&"conservative_inframe_deletion"))
                     {
-                        expected_one_of.push(String::from("inframe_deletion"));
+                        expected_one_of.push("inframe_deletion");
                     }
 
                     // Try to find a direct match.
                     let found_one = record_csqs.iter().any(|csq| expected_one_of.contains(csq));
+
+                    // vep sometimes only reports a coding_sequence_variant, so we accept anything
+                    let found_one = found_one
+                        || path_tsv.contains(".vep")
+                            && (record_csqs == ["coding_sequence_variant"]
+                                && !expected_one_of.is_empty());
+
                     // It is common that the other tool predicts a frameshift variant while the actual prediction
                     // is stop_gained or stop_lost.  We thus also check for this case and allow it.
                     let found_one = found_one
-                        || (record_csqs.contains(&String::from("frameshift_variant"))
-                            && (expected_one_of.contains(&String::from("stop_gained")))
-                            || expected_one_of.contains(&String::from("stop_lost")));
+                        || (record_csqs.contains(&"frameshift_variant")
+                            && (expected_one_of.contains(&"stop_gained"))
+                            || expected_one_of.contains(&"stop_lost"));
                     // VEP does not differentiate between disruptive and conservative inframe deletions and insertions.
                     let found_one = found_one
-                        || (record_csqs.contains(&String::from("inframe_deletion"))
-                            && (expected_one_of
-                                .contains(&String::from("disruptive_inframe_deletion")))
-                            || expected_one_of
-                                .contains(&String::from("conservative_inframe_deletion")))
-                        || (record_csqs.contains(&String::from("inframe_insertion"))
-                            && (expected_one_of
-                                .contains(&String::from("disruptive_inframe_insertion")))
-                            || expected_one_of
-                                .contains(&String::from("conservative_inframe_insertion")));
+                        || (record_csqs.contains(&"inframe_deletion")
+                            && (expected_one_of.contains(&"disruptive_inframe_deletion")
+                                || expected_one_of.contains(&"conservative_inframe_deletion")))
+                        || (record_csqs.contains(&"inframe_insertion")
+                            && (expected_one_of.contains(&"disruptive_inframe_insertion")
+                                || expected_one_of.contains(&"conservative_inframe_insertion")));
                     // NB: We cannot predict 5_prime_UTR_premature_start_codon_gain_variant yet. For now, we
                     // also accept 5_prime_UTR_variant.
                     let found_one = found_one
-                        || ((expected_one_of.contains(&String::from("5_prime_UTR_exon_variant"))
-                            || expected_one_of
-                                .contains(&String::from("5_prime_UTR_intron_variant")))
-                            && (record_csqs.contains(&String::from(
-                                "5_prime_UTR_premature_start_codon_gain_variant",
-                            ))));
+                        || ((expected_one_of.contains(&"5_prime_UTR_exon_variant")
+                            || expected_one_of.contains(&"5_prime_UTR_intron_variant"))
+                            && (record_csqs
+                                .contains(&"5_prime_UTR_premature_start_codon_gain_variant")));
                     // VEP predicts `splice_donor_5th_base_variant` rather than `splice_region_variant`.
                     // Same for `splice_donor_region_variant`.
                     let found_one = found_one
-                        || (expected_one_of.contains(&String::from("splice_region_variant"))
-                            && (record_csqs
-                                .contains(&String::from("splice_donor_5th_base_variant"))
-                                || record_csqs
-                                    .contains(&String::from("splice_donor_region_variant"))));
+                        || (expected_one_of.contains(&"splice_region_variant")
+                            && (record_csqs.contains(&"splice_donor_5th_base_variant")
+                                || record_csqs.contains(&"splice_donor_region_variant")));
                     // In the case of insertions at the end of an exon, VEP predicts `splice_region_variant`
                     // while we predict `splice_donor_variant`, same for start.
                     let found_one = found_one
-                        || (expected_one_of.contains(&String::from("splice_donor_variant"))
-                            || expected_one_of.contains(&String::from("splice_acceptor_variant")))
-                            && (record_csqs.contains(&String::from("splice_region_variant")));
+                        || (expected_one_of.contains(&"splice_donor_variant")
+                            || expected_one_of.contains(&"splice_acceptor_variant"))
+                            && (record_csqs.contains(&"splice_region_variant"));
                     // VEP sometimes mispredicts disruptive inframe deletion as missense...
                     // cf. https://github.com/Ensembl/ensembl-vep/issues/1388
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("disruptive_inframe_deletion"))
-                            && (record_csqs.contains(&String::from("missense_variant")));
+                        || expected_one_of.contains(&"disruptive_inframe_deletion")
+                            && (record_csqs.contains(&"missense_variant"));
                     // VEP does not provide `exon_loss_variant`, so we also accept `inframe_deletion` and
                     // `splice_region_variant` (BRA1 test case).
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("exon_loss_variant"))
-                            && (record_csqs.contains(&String::from("inframe_deletion"))
-                                || record_csqs.contains(&String::from("splice_region_variant")));
+                        || expected_one_of.contains(&"exon_loss_variant")
+                            && (record_csqs.contains(&"inframe_deletion")
+                                || record_csqs.contains(&"splice_region_variant"));
                     // On BRCA1, there is a case where VEP predicts `protein_altering_variant` rather than
                     // `disruptive_inframe_deletion`.  We accept this as well.
                     let found_one = found_one
-                        || (expected_one_of.contains(&String::from("disruptive_inframe_deletion"))
-                            || expected_one_of.contains(&String::from("inframe_indel")))
-                            && (record_csqs.contains(&String::from("protein_altering_variant")));
+                        || (expected_one_of.contains(&"disruptive_inframe_deletion")
+                            || expected_one_of.contains(&"inframe_indel"))
+                            && (record_csqs.contains(&"protein_altering_variant"));
                     // In the case of `GRCh37:17:41258543:T:TA`, the `hgvs` prediction is `c.-1_1insT` and
                     // `p.Met1?` which leads to `start_lost` while VEP predicts `5_prime_UTR_variant`.
                     // This may be a bug in `hgvs` and we don't change this for now.  We accept the call
                     // by VEP, of course.
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("start_lost"))
-                            && (record_csqs.contains(&String::from("5_prime_UTR_variant")));
+                        || expected_one_of.contains(&"start_lost")
+                            && (record_csqs.contains(&"5_prime_UTR_variant"));
                     // We have specialized {5,3}_prime_UTR_{exon,intron}_variant handling, while
                     // vep and snpEff do not
                     let found_one = found_one
-                        || record_csqs.contains(&String::from("5_prime_UTR_variant"))
-                            && (expected_one_of
-                                .contains(&String::from("5_prime_UTR_exon_variant"))
-                                || expected_one_of
-                                    .contains(&String::from("5_prime_UTR_intron_variant")));
+                        || record_csqs.contains(&"5_prime_UTR_variant")
+                            && (expected_one_of.contains(&"5_prime_UTR_exon_variant")
+                                || expected_one_of.contains(&"5_prime_UTR_intron_variant"));
                     let found_one = found_one
-                        || record_csqs.contains(&String::from("3_prime_UTR_variant"))
-                            && (expected_one_of
-                                .contains(&String::from("3_prime_UTR_exon_variant"))
-                                || expected_one_of
-                                    .contains(&String::from("3_prime_UTR_intron_variant")));
+                        || record_csqs.contains(&"3_prime_UTR_variant")
+                            && (expected_one_of.contains(&"3_prime_UTR_exon_variant")
+                                || expected_one_of.contains(&"3_prime_UTR_intron_variant"));
                     // an inframe_indel can be a missense_variant if it is an MNV (which we do not explicitly check here)
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("inframe_indel"))
-                            && (record_csqs.contains(&String::from("missense_variant")));
+                        || expected_one_of.contains(&"inframe_indel")
+                            && (record_csqs.contains(&"missense_variant"));
                     // inframe_indel also is a superclass of *_inframe_{deletion, insertion}
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("inframe_indel"))
+                        || expected_one_of.contains(&"inframe_indel")
                             && [
                                 "disruptive_inframe_deletion",
                                 "conservative_inframe_deletion",
@@ -1723,45 +2026,42 @@ mod test {
                                 "inframe_insertion",
                             ]
                             .iter()
-                            .any(|c| record_csqs.contains(&String::from(*c)));
+                            .any(|c| record_csqs.contains(c));
                     // SnpEff has a different interpretation of disruptive/conservative inframe deletions.
                     // We thus allow both.
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("disruptive_inframe_deletion"))
-                            && (record_csqs
-                                .contains(&String::from("conservative_inframe_deletion")))
-                        || expected_one_of.contains(&String::from("disruptive_inframe_insertion"))
-                            && (record_csqs
-                                .contains(&String::from("conservative_inframe_insertion")));
+                        || expected_one_of.contains(&"disruptive_inframe_deletion")
+                            && (record_csqs.contains(&"conservative_inframe_deletion"))
+                        || expected_one_of.contains(&"disruptive_inframe_insertion")
+                            && (record_csqs.contains(&"conservative_inframe_insertion"));
                     // SnpEff may not predict `splice_region_variant` for 5' UTR correctly, so we
                     // allow this.
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("splice_region_variant"))
-                            && (record_csqs.contains(&String::from("5_prime_UTR_variant")));
+                        || expected_one_of.contains(&"splice_region_variant")
+                            && (record_csqs.contains(&"5_prime_UTR_variant"));
                     // SnpEff does not predict `splice_polypyrimidine_tract_variant`
                     let found_one = found_one
-                        || expected_one_of
-                            .contains(&String::from("splice_polypyrimidine_tract_variant"))
-                            && (record_csqs.contains(&String::from("splice_region_variant"))
-                                || record_csqs.contains(&String::from("intron_variant")));
+                        || expected_one_of.contains(&"splice_polypyrimidine_tract_variant")
+                            && (record_csqs.contains(&"splice_region_variant")
+                                || record_csqs.contains(&"intron_variant"));
                     // For `GRCh37:3:193366573:A:ATATTGCCTAGAATGAACT`, SnpEff predicts
                     // `stop_gained` while this rather is a intron variant.  We skip this variant.
                     let found_one = found_one
-                        || record_csqs.contains(&String::from("stop_gained"))
+                        || record_csqs.contains(&"stop_gained")
                             && record.var == "3-193366573-A-ATATTGCCTAGAATGAACT";
                     // For `GRCh37:3:193409913:ATAAAT:A`, there appears to be a model error
                     // in SnpEff as it predicts `exon_loss`.  We skip this variant.
                     let found_one = found_one
-                        || record_csqs.contains(&String::from("exon_loss_variant"))
+                        || record_csqs.contains(&"exon_loss_variant")
                             && record.var == "3-193409913-ATAAAT-A";
                     // SnpEff may predict `pMet1.?` as `initiator_codon_variant` rather than `start_lost`.
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("start_lost"))
-                            && (record_csqs.contains(&String::from("initiator_codon_variant")));
+                        || expected_one_of.contains(&"start_lost")
+                            && (record_csqs.contains(&"initiator_codon_variant"));
                     // Similarly, SnpEff may predict `c.-1_1` as `start_retained` rather than `start_lost`.
                     let found_one = found_one
-                        || expected_one_of.contains(&String::from("start_lost"))
-                            && (record_csqs.contains(&String::from("start_retained_variant")));
+                        || expected_one_of.contains(&"start_lost")
+                            && (record_csqs.contains(&"start_retained_variant"));
 
                     assert!(
                         found_one,
diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap
index 80f398d7..4a50aa78 100644
--- a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap
+++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap
@@ -6,6 +6,7 @@ expression: res
     Alt:
       alternative: C
   consequences:
+    - splice_region_variant
     - synonymous_variant
   putative_impact: low
   gene_symbol: BRCA1
@@ -38,6 +39,7 @@ expression: res
     Alt:
       alternative: C
   consequences:
+    - splice_region_variant
     - synonymous_variant
   putative_impact: low
   gene_symbol: BRCA1
@@ -69,6 +71,7 @@ expression: res
     Alt:
       alternative: C
   consequences:
+    - splice_region_variant
     - synonymous_variant
   putative_impact: low
   gene_symbol: BRCA1
@@ -101,6 +104,7 @@ expression: res
       alternative: C
   consequences:
     - missense_variant
+    - splice_region_variant
   putative_impact: moderate
   gene_symbol: BRCA1
   gene_id: "HGNC:1100"
@@ -131,6 +135,7 @@ expression: res
     Alt:
       alternative: C
   consequences:
+    - splice_region_variant
     - synonymous_variant
   putative_impact: low
   gene_symbol: BRCA1
diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap
index 61a05ee5..1528da32 100644
--- a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap
+++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap
@@ -7,6 +7,7 @@ expression: res
       alternative: C
   consequences:
     - missense_variant
+    - splice_region_variant
   putative_impact: moderate
   gene_symbol: BRCA1
   gene_id: "HGNC:1100"
@@ -39,6 +40,7 @@ expression: res
       alternative: C
   consequences:
     - missense_variant
+    - splice_region_variant
   putative_impact: moderate
   gene_symbol: BRCA1
   gene_id: "HGNC:1100"
@@ -70,6 +72,7 @@ expression: res
       alternative: C
   consequences:
     - missense_variant
+    - splice_region_variant
   putative_impact: moderate
   gene_symbol: BRCA1
   gene_id: "HGNC:1100"
@@ -101,6 +104,7 @@ expression: res
       alternative: C
   consequences:
     - missense_variant
+    - splice_region_variant
   putative_impact: moderate
   gene_symbol: BRCA1
   gene_id: "HGNC:1100"
@@ -132,6 +136,7 @@ expression: res
       alternative: C
   consequences:
     - missense_variant
+    - splice_region_variant
   putative_impact: moderate
   gene_symbol: BRCA1
   gene_id: "HGNC:1100"
diff --git a/tests/data/annotate/db/grch38/GRCh38-ensembl.disagreement-subset.txs.bin.zst b/tests/data/annotate/db/grch38/GRCh38-ensembl.disagreement-subset.txs.bin.zst
new file mode 100644
index 00000000..88aa2b7a
--- /dev/null
+++ b/tests/data/annotate/db/grch38/GRCh38-ensembl.disagreement-subset.txs.bin.zst
@@ -0,0 +1,3 @@
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+size 263383
diff --git a/tests/data/annotate/seqvars/vep.disagreement-cases.expected.vcf b/tests/data/annotate/seqvars/vep.disagreement-cases.expected.vcf
new file mode 100644
index 00000000..b4bc1e47
--- /dev/null
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diff --git a/tests/data/annotate/seqvars/vep.disagreement-cases.vcf b/tests/data/annotate/seqvars/vep.disagreement-cases.vcf
new file mode 100644
index 00000000..105969ab
--- /dev/null
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