From 339b445b50836045dc41a9d19bee36de34653a0c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 8 Feb 2024 11:04:28 +0000
Subject: [PATCH 1/2] build(deps): bump the noodles group with 7 updates

Bumps the noodles group with 7 updates:

| Package | From | To |
| --- | --- | --- |
| [annonars](https://github.com/varfish-org/annonars) | `0.30.1` | `0.34.1` |
| [noodles-bgzf](https://github.com/zaeleus/noodles) | `0.25.0` | `0.26.0` |
| [noodles-core](https://github.com/zaeleus/noodles) | `0.12.0` | `0.14.0` |
| [noodles-csi](https://github.com/zaeleus/noodles) | `0.28.0` | `0.30.0` |
| [noodles-fasta](https://github.com/zaeleus/noodles) | `0.30.0` | `0.32.0` |
| [noodles-tabix](https://github.com/zaeleus/noodles) | `0.34.0` | `0.36.0` |
| [noodles-vcf](https://github.com/zaeleus/noodles) | `0.47.0` | `0.49.0` |


Updates `annonars` from 0.30.1 to 0.34.1
- [Release notes](https://github.com/varfish-org/annonars/releases)
- [Changelog](https://github.com/varfish-org/annonars/blob/main/CHANGELOG.md)
- [Commits](https://github.com/varfish-org/annonars/compare/v0.30.1...v0.34.1)

Updates `noodles-bgzf` from 0.25.0 to 0.26.0
- [Commits](https://github.com/zaeleus/noodles/compare/noodles-bgzf-0.25.0...noodles-bgzf-0.26.0)

Updates `noodles-core` from 0.12.0 to 0.14.0
- [Commits](https://github.com/zaeleus/noodles/compare/noodles-core-0.12.0...noodles-core-0.14.0)

Updates `noodles-csi` from 0.28.0 to 0.30.0
- [Commits](https://github.com/zaeleus/noodles/compare/noodles-csi-0.28.0...noodles-csi-0.30.0)

Updates `noodles-fasta` from 0.30.0 to 0.32.0
- [Commits](https://github.com/zaeleus/noodles/compare/noodles-fasta-0.30.0...noodles-fasta-0.32.0)

Updates `noodles-tabix` from 0.34.0 to 0.36.0
- [Commits](https://github.com/zaeleus/noodles/compare/noodles-tabix-0.34.0...noodles-tabix-0.36.0)

Updates `noodles-vcf` from 0.47.0 to 0.49.0
- [Commits](https://github.com/zaeleus/noodles/compare/noodles-vcf-0.47.0...noodles-vcf-0.49.0)

---
updated-dependencies:
- dependency-name: annonars
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: noodles
- dependency-name: noodles-bgzf
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: noodles
- dependency-name: noodles-core
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: noodles
- dependency-name: noodles-csi
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: noodles
- dependency-name: noodles-fasta
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: noodles
- dependency-name: noodles-tabix
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: noodles
- dependency-name: noodles-vcf
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: noodles
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Cargo.lock | 144 +++++++++++++++++++++++++++++++++++++++++------------
 Cargo.toml |  14 +++---
 2 files changed, 120 insertions(+), 38 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index ba2a5660..f04efd47 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -267,9 +267,9 @@ dependencies = [
 
 [[package]]
 name = "annonars"
-version = "0.30.1"
+version = "0.34.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e41d0f0c12a8e870bc2b0152482fc9581efb832ec016d822e62456a19a0f22c9"
+checksum = "9595f45b904e6392e7b8f02cfd5a69b569e8bf71128364547ec2753827bc5f8f"
 dependencies = [
  "actix-web",
  "anyhow",
@@ -284,17 +284,18 @@ dependencies = [
  "csv",
  "enum-map",
  "env_logger",
+ "erased-serde",
  "flate2",
  "indexmap 2.2.2",
  "indicatif",
  "log",
  "noodles-bed",
- "noodles-bgzf",
- "noodles-core",
- "noodles-csi",
+ "noodles-bgzf 0.25.0",
+ "noodles-core 0.12.0",
+ "noodles-csi 0.28.0",
  "noodles-gff",
- "noodles-tabix",
- "noodles-vcf",
+ "noodles-tabix 0.34.0",
+ "noodles-vcf 0.47.0",
  "pbjson",
  "pbjson-build",
  "pbjson-types",
@@ -1394,6 +1395,15 @@ version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
 
+[[package]]
+name = "erased-serde"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "55d05712b2d8d88102bc9868020c9e5c7a1f5527c452b9b97450a1d006140ba7"
+dependencies = [
+ "serde",
+]
+
 [[package]]
 name = "errno"
 version = "0.3.8"
@@ -2226,12 +2236,12 @@ dependencies = [
  "lazy_static",
  "log",
  "nom",
- "noodles-bgzf",
- "noodles-core",
- "noodles-csi",
- "noodles-fasta",
- "noodles-tabix",
- "noodles-vcf",
+ "noodles-bgzf 0.26.0",
+ "noodles-core 0.14.0",
+ "noodles-csi 0.30.0",
+ "noodles-fasta 0.32.0",
+ "noodles-tabix 0.36.0",
+ "noodles-vcf 0.49.0",
  "parse-display",
  "pbjson",
  "pbjson-build",
@@ -2387,7 +2397,7 @@ version = "0.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "deba180b7b94c524307da91d5bc983e0ccb9a08c4e24384cc8f93e0210af254a"
 dependencies = [
- "noodles-core",
+ "noodles-core 0.12.0",
 ]
 
 [[package]]
@@ -2395,6 +2405,18 @@ name = "noodles-bgzf"
 version = "0.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7d578e5a173cbfac77295db4188c959966ce24a3364e009d363170d1ed44066a"
+dependencies = [
+ "byteorder",
+ "bytes",
+ "crossbeam-channel",
+ "flate2",
+]
+
+[[package]]
+name = "noodles-bgzf"
+version = "0.26.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8970db2e84adb1007377dd3988258d7a64e3fc4c05602ebf94e1f8cba207c030"
 dependencies = [
  "byteorder",
  "bytes",
@@ -2412,6 +2434,12 @@ version = "0.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "94fbe3192fe33acacabaedd387657f39b0fc606f1996d546db0dfe14703b843a"
 
+[[package]]
+name = "noodles-core"
+version = "0.14.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7336c3be652de4e05444c9b12a32331beb5ba3316e8872d92bfdd8ef3b06c282"
+
 [[package]]
 name = "noodles-csi"
 version = "0.28.0"
@@ -2421,8 +2449,21 @@ dependencies = [
  "bit-vec",
  "byteorder",
  "indexmap 2.2.2",
- "noodles-bgzf",
- "noodles-core",
+ "noodles-bgzf 0.25.0",
+ "noodles-core 0.12.0",
+]
+
+[[package]]
+name = "noodles-csi"
+version = "0.30.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a60dfe0919f7ecbd081a82eb1d32e8f89f9041932d035fe8309073c8c01277bf"
+dependencies = [
+ "bit-vec",
+ "byteorder",
+ "indexmap 2.2.2",
+ "noodles-bgzf 0.26.0",
+ "noodles-core 0.14.0",
 ]
 
 [[package]]
@@ -2433,8 +2474,20 @@ checksum = "310dcfb61e8e2cafb65d9da4b329a98a390f2b570c17599a7f4639328cfb3e2c"
 dependencies = [
  "bytes",
  "memchr",
- "noodles-bgzf",
- "noodles-core",
+ "noodles-bgzf 0.25.0",
+ "noodles-core 0.12.0",
+]
+
+[[package]]
+name = "noodles-fasta"
+version = "0.32.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ebb3e83e0f112d3482f5234a1eb219081f12cc3aab38a9eba00ef1846b43b63b"
+dependencies = [
+ "bytes",
+ "memchr",
+ "noodles-bgzf 0.26.0",
+ "noodles-core 0.14.0",
 ]
 
 [[package]]
@@ -2444,9 +2497,9 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "fec62bd9306cce6d551c9c7075beca940aec283efd18648b6d04860b693fd092"
 dependencies = [
  "indexmap 2.2.2",
- "noodles-bgzf",
- "noodles-core",
- "noodles-csi",
+ "noodles-bgzf 0.25.0",
+ "noodles-core 0.12.0",
+ "noodles-csi 0.28.0",
  "percent-encoding",
 ]
 
@@ -2459,9 +2512,23 @@ dependencies = [
  "bit-vec",
  "byteorder",
  "indexmap 2.2.2",
- "noodles-bgzf",
- "noodles-core",
- "noodles-csi",
+ "noodles-bgzf 0.25.0",
+ "noodles-core 0.12.0",
+ "noodles-csi 0.28.0",
+]
+
+[[package]]
+name = "noodles-tabix"
+version = "0.36.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cc1ab29335a68d0c2bdf41460a67714ca69e23a1cbeb950ac5c38a9afa446a62"
+dependencies = [
+ "bit-vec",
+ "byteorder",
+ "indexmap 2.2.2",
+ "noodles-bgzf 0.26.0",
+ "noodles-core 0.14.0",
+ "noodles-csi 0.30.0",
  "tokio",
 ]
 
@@ -2470,14 +2537,29 @@ name = "noodles-vcf"
 version = "0.47.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "610f14797affe3ecc3687732e310ff508c909dd18d3b12d0cd135bc4cc5593e9"
+dependencies = [
+ "indexmap 2.2.2",
+ "memchr",
+ "noodles-bgzf 0.25.0",
+ "noodles-core 0.12.0",
+ "noodles-csi 0.28.0",
+ "noodles-tabix 0.34.0",
+ "percent-encoding",
+]
+
+[[package]]
+name = "noodles-vcf"
+version = "0.49.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2e1f2fa749afaccadc596ec55ccb7bdcd8101fa79f8382384223c0dbae3e245b"
 dependencies = [
  "futures",
  "indexmap 2.2.2",
  "memchr",
- "noodles-bgzf",
- "noodles-core",
- "noodles-csi",
- "noodles-tabix",
+ "noodles-bgzf 0.26.0",
+ "noodles-core 0.14.0",
+ "noodles-csi 0.30.0",
+ "noodles-tabix 0.36.0",
  "percent-encoding",
  "tokio",
 ]
@@ -3377,9 +3459,9 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f2952aee50ad05e57127f0857aa9553bbce29aea59817da2127c34ce09f6dd65"
 dependencies = [
  "chrono",
- "noodles-bgzf",
- "noodles-core",
- "noodles-fasta",
+ "noodles-bgzf 0.25.0",
+ "noodles-core 0.12.0",
+ "noodles-fasta 0.30.0",
  "rusqlite",
  "thiserror",
  "tracing",
diff --git a/Cargo.toml b/Cargo.toml
index afa7beab..c3cd9baa 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -27,7 +27,7 @@ path = "src/main.rs"
 
 [dependencies]
 actix-web = "4.5"
-annonars = "0.30"
+annonars = "0.34"
 anyhow = "1.0"
 async-compression = { version = "0.4", features = ["tokio", "gzip"] }
 bgzip = "0.3"
@@ -51,12 +51,12 @@ jsonl = "4.0"
 lazy_static = "1.4"
 log = "0.4"
 nom = "7.1"
-noodles-bgzf = { version = "0.25", features = ["async"] }
-noodles-core = "0.12"
-noodles-csi = "0.28"
-noodles-fasta = "0.30"
-noodles-tabix = "0.34"
-noodles-vcf = { version = "0.47", features = ["async"] }
+noodles-bgzf = { version = "0.26", features = ["async"] }
+noodles-core = "0.14"
+noodles-csi = "0.30"
+noodles-fasta = "0.32"
+noodles-tabix = "0.36"
+noodles-vcf = { version = "0.49", features = ["async"] }
 parse-display = "0.9"
 procfs = "0.16"
 prost = "0.12"

From a7b0ce40ce63fc88b945cade66e3d44f1f1d6799 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Thu, 8 Feb 2024 17:06:33 +0100
Subject: [PATCH 2/2] wip

---
 Cargo.lock | 842 +++++++++++++++++++++--------------------------------
 Cargo.toml |  14 +-
 fixit.sh   |   8 +
 3 files changed, 349 insertions(+), 515 deletions(-)
 create mode 100644 fixit.sh

diff --git a/Cargo.lock b/Cargo.lock
index f04efd47..006010dd 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -4,11 +4,11 @@ version = 3
 
 [[package]]
 name = "actix-codec"
-version = "0.5.1"
+version = "0.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "617a8268e3537fe1d8c9ead925fca49ef6400927ee7bc26750e90ecee14ce4b8"
+checksum = "5f7b0a21988c1bf877cf4759ef5ddaac04c1c9fe808c9142ecb78ba97d97a28a"
 dependencies = [
- "bitflags 1.3.2",
+ "bitflags 2.4.2",
  "bytes",
  "futures-core",
  "futures-sink",
@@ -29,9 +29,9 @@ dependencies = [
  "actix-rt",
  "actix-service",
  "actix-utils",
- "ahash 0.8.6",
+ "ahash 0.8.7",
  "base64",
- "bitflags 2.4.1",
+ "bitflags 2.4.2",
  "brotli",
  "bytes",
  "bytestring",
@@ -70,9 +70,9 @@ dependencies = [
 
 [[package]]
 name = "actix-router"
-version = "0.5.1"
+version = "0.5.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d66ff4d247d2b160861fa2866457e85706833527840e4133f8f49aa423a38799"
+checksum = "d22475596539443685426b6bdadb926ad0ecaefdfc5fb05e5e3441f15463c511"
 dependencies = [
  "bytestring",
  "http",
@@ -144,7 +144,7 @@ dependencies = [
  "actix-service",
  "actix-utils",
  "actix-web-codegen",
- "ahash 0.8.6",
+ "ahash 0.8.7",
  "bytes",
  "bytestring",
  "cfg-if",
@@ -209,9 +209,9 @@ dependencies = [
 
 [[package]]
 name = "ahash"
-version = "0.8.6"
+version = "0.8.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a"
+checksum = "77c3a9648d43b9cd48db467b3f87fdd6e146bcc88ab0180006cef2179fe11d01"
 dependencies = [
  "cfg-if",
  "getrandom",
@@ -267,9 +267,9 @@ dependencies = [
 
 [[package]]
 name = "annonars"
-version = "0.34.1"
+version = "0.35.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9595f45b904e6392e7b8f02cfd5a69b569e8bf71128364547ec2753827bc5f8f"
+checksum = "416b073dbcbd14a2b552288cc1a1cf10fdac357886c9bc671e47cb634b218649"
 dependencies = [
  "actix-web",
  "anyhow",
@@ -286,16 +286,16 @@ dependencies = [
  "env_logger",
  "erased-serde",
  "flate2",
- "indexmap 2.2.2",
+ "indexmap",
  "indicatif",
  "log",
  "noodles-bed",
- "noodles-bgzf 0.25.0",
- "noodles-core 0.12.0",
- "noodles-csi 0.28.0",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
  "noodles-gff",
- "noodles-tabix 0.34.0",
- "noodles-vcf 0.47.0",
+ "noodles-tabix",
+ "noodles-vcf",
  "pbjson",
  "pbjson-build",
  "pbjson-types",
@@ -308,7 +308,7 @@ dependencies = [
  "serde",
  "serde_json",
  "serde_with",
- "strum 0.25.0",
+ "strum 0.26.1",
  "thiserror",
  "tracing",
  "tracing-subscriber",
@@ -316,9 +316,9 @@ dependencies = [
 
 [[package]]
 name = "anstream"
-version = "0.6.7"
+version = "0.6.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4cd2405b3ac1faab2990b74d728624cd9fd115651fcecc7c2d8daf01376275ba"
+checksum = "6e2e1ebcb11de5c03c67de28a7df593d32191b44939c482e97702baaaa6ab6a5"
 dependencies = [
  "anstyle",
  "anstyle-parse",
@@ -330,36 +330,36 @@ dependencies = [
 
 [[package]]
 name = "anstyle"
-version = "1.0.4"
+version = "1.0.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7079075b41f533b8c61d2a4d073c4676e1f8b249ff94a393b0595db304e0dd87"
+checksum = "8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.2"
+version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "317b9a89c1868f5ea6ff1d9539a69f45dffc21ce321ac1fd1160dfa48c8e2140"
+checksum = "c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.0.0"
+version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b"
+checksum = "e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648"
 dependencies = [
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.1"
+version = "3.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f0699d10d2f4d628a98ee7b57b289abbc98ff3bad977cb3152709d4bf2330628"
+checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7"
 dependencies = [
  "anstyle",
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -411,7 +411,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1ca33f4bc4ed1babef42cad36cc1f51fa88be00420404e5b1e80ab1b18f7678c"
 dependencies = [
  "concurrent-queue",
- "event-listener 4.0.0",
+ "event-listener 4.0.3",
  "event-listener-strategy",
  "futures-core",
  "pin-project-lite",
@@ -436,26 +436,26 @@ version = "1.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "17ae5ebefcc48e7452b4987947920dac9450be1110cadf34d1b8c116bdbaf97c"
 dependencies = [
- "async-lock 3.1.2",
+ "async-lock 3.3.0",
  "async-task",
  "concurrent-queue",
  "fastrand 2.0.1",
- "futures-lite 2.0.1",
+ "futures-lite 2.2.0",
  "slab",
 ]
 
 [[package]]
 name = "async-global-executor"
-version = "2.4.0"
+version = "2.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9b4353121d5644cdf2beb5726ab752e79a8db1ebb52031770ec47db31d245526"
+checksum = "05b1b633a2115cd122d73b955eadd9916c18c8f510ec9cd1686404c60ad1c29c"
 dependencies = [
  "async-channel 2.1.1",
  "async-executor",
- "async-io 2.2.1",
- "async-lock 3.1.2",
+ "async-io 2.3.1",
+ "async-lock 3.3.0",
  "blocking",
- "futures-lite 2.0.1",
+ "futures-lite 2.2.0",
  "once_cell",
 ]
 
@@ -481,18 +481,18 @@ dependencies = [
 
 [[package]]
 name = "async-io"
-version = "2.2.1"
+version = "2.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d6d3b15875ba253d1110c740755e246537483f152fa334f91abd7fe84c88b3ff"
+checksum = "8f97ab0c5b00a7cdbe5a371b9a782ee7be1316095885c8a4ea1daf490eb0ef65"
 dependencies = [
- "async-lock 3.1.2",
+ "async-lock 3.3.0",
  "cfg-if",
  "concurrent-queue",
  "futures-io",
- "futures-lite 2.0.1",
+ "futures-lite 2.2.0",
  "parking",
- "polling 3.3.1",
- "rustix 0.38.26",
+ "polling 3.4.0",
+ "rustix 0.38.31",
  "slab",
  "tracing",
  "windows-sys 0.52.0",
@@ -509,11 +509,11 @@ dependencies = [
 
 [[package]]
 name = "async-lock"
-version = "3.1.2"
+version = "3.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dea8b3453dd7cc96711834b75400d671b73e3656975fa68d9f277163b7f7e316"
+checksum = "d034b430882f8381900d3fe6f0aaa3ad94f2cb4ac519b429692a1bc2dda4ae7b"
 dependencies = [
- "event-listener 4.0.0",
+ "event-listener 4.0.3",
  "event-listener-strategy",
  "pin-project-lite",
 ]
@@ -547,15 +547,15 @@ dependencies = [
 
 [[package]]
 name = "async-task"
-version = "4.5.0"
+version = "4.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b4eb2cdb97421e01129ccb49169d8279ed21e829929144f4a22a6e54ac549ca1"
+checksum = "fbb36e985947064623dbd357f727af08ffd077f93d696782f3c56365fa2e2799"
 
 [[package]]
 name = "async-trait"
-version = "0.1.74"
+version = "0.1.77"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a66537f1bb974b254c98ed142ff995236e81b9d0fe4db0575f46612cb15eb0f9"
+checksum = "c980ee35e870bd1a4d2c8294d4c04d0499e67bca1e4b5cefcc693c2fa00caea9"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -597,9 +597,9 @@ checksum = "4c7f02d4ea65f2c1853089ffd8d2787bdbc63de2f0d29dedbcf8ccdfa0ccd4cf"
 
 [[package]]
 name = "base64"
-version = "0.21.5"
+version = "0.21.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "35636a1494ede3b646cc98f74f8e62c773a38a659ebc777a2cf26b9b74171df9"
+checksum = "9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567"
 
 [[package]]
 name = "bgzip"
@@ -655,7 +655,7 @@ dependencies = [
  "itertools",
  "itertools-num",
  "lazy_static",
- "multimap",
+ "multimap 0.9.1",
  "ndarray",
  "newtype_derive",
  "num-integer",
@@ -695,7 +695,7 @@ checksum = "82c91bd0b62cec4b6317445506ed4947a53c320942a681c5a086f4d576aa4c99"
 dependencies = [
  "enum-map",
  "flate2",
- "indexmap 2.2.2",
+ "indexmap",
  "lazy_static",
  "serde",
  "serde_json",
@@ -724,9 +724,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
 
 [[package]]
 name = "bitflags"
-version = "2.4.1"
+version = "2.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07"
+checksum = "ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf"
 
 [[package]]
 name = "bitvec"
@@ -756,11 +756,11 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6a37913e8dc4ddcc604f0c6d3bf2887c995153af3611de9e23c352b44c1b9118"
 dependencies = [
  "async-channel 2.1.1",
- "async-lock 3.1.2",
+ "async-lock 3.3.0",
  "async-task",
  "fastrand 2.0.1",
  "futures-io",
- "futures-lite 2.0.1",
+ "futures-lite 2.2.0",
  "piper",
  "tracing",
 ]
@@ -845,9 +845,9 @@ dependencies = [
 
 [[package]]
 name = "bytecheck"
-version = "0.6.11"
+version = "0.6.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8b6372023ac861f6e6dc89c8344a8f398fb42aaba2b5dbc649ca0c0e9dbcb627"
+checksum = "23cdc57ce23ac53c931e88a43d06d070a6fd142f2617be5855eb75efc9beb1c2"
 dependencies = [
  "bytecheck_derive",
  "ptr_meta",
@@ -856,9 +856,9 @@ dependencies = [
 
 [[package]]
 name = "bytecheck_derive"
-version = "0.6.11"
+version = "0.6.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a7ec4c6f261935ad534c0c22dbef2201b45918860eb1c574b972bd213a76af61"
+checksum = "3db406d29fbcd95542e92559bed4d8ad92636d1ca8b3b72ede10b4bcc010e659"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -873,9 +873,9 @@ checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205"
 
 [[package]]
 name = "bytemuck"
-version = "1.14.0"
+version = "1.14.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "374d28ec25809ee0e23827c2ab573d729e293f281dfe393500e7ad618baa61c6"
+checksum = "ea31d69bda4949c1c1562c1e6f042a1caefac98cdc8a298260a2ff41c1e2d42b"
 
 [[package]]
 name = "byteorder"
@@ -957,9 +957,9 @@ dependencies = [
 
 [[package]]
 name = "clang-sys"
-version = "1.6.1"
+version = "1.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c688fc74432808e3eb684cae8830a86be1d66a2bd58e1f248ed0960a590baf6f"
+checksum = "67523a3b4be3ce1989d607a828d036249522dd9c1c8de7f4dd2dae43a37369d1"
 dependencies = [
  "glob",
  "libc",
@@ -968,9 +968,9 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.4.17"
+version = "4.4.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "80932e03c33999b9235edb8655bc9df3204adc9887c2f95b50cb1deb9fd54253"
+checksum = "1e578d6ec4194633722ccf9544794b71b1385c3c027efe0c55db226fc880865c"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -988,9 +988,9 @@ dependencies = [
 
 [[package]]
 name = "clap_builder"
-version = "4.4.17"
+version = "4.4.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d6c0db58c659eef1c73e444d298c27322a1b52f6927d2ad470c0c0f96fa7b8fa"
+checksum = "4df4df40ec50c46000231c914968278b1eb05098cf8f1b3a518a95030e71d1c7"
 dependencies = [
  "anstream",
  "anstyle",
@@ -1024,24 +1024,24 @@ checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7"
 
 [[package]]
 name = "concurrent-queue"
-version = "2.3.0"
+version = "2.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f057a694a54f12365049b0958a1685bb52d567f5593b355fbf685838e873d400"
+checksum = "d16048cd947b08fa32c24458a22f5dc5e835264f689f4f5653210c69fd107363"
 dependencies = [
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "console"
-version = "0.15.7"
+version = "0.15.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c926e00cc70edefdc64d3a5ff31cc65bb97a3460097762bd23afb4d8145fccf8"
+checksum = "0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb"
 dependencies = [
  "encode_unicode",
  "lazy_static",
  "libc",
  "unicode-width",
- "windows-sys 0.45.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -1069,9 +1069,9 @@ checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f"
 
 [[package]]
 name = "cpufeatures"
-version = "0.2.11"
+version = "0.2.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ce420fe07aecd3e67c5f910618fe65e94158f6dcc0adf44e00d69ce2bdfe0fd0"
+checksum = "53fe5e26ff1b7aef8bca9c6080520cfb8d9333c7568e1829cef191a9723e5504"
 dependencies = [
  "libc",
 ]
@@ -1087,46 +1087,37 @@ dependencies = [
 
 [[package]]
 name = "crossbeam-channel"
-version = "0.5.8"
+version = "0.5.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a33c2bf77f2df06183c3aa30d1e96c0695a313d4f9c453cc3762a6db39f99200"
+checksum = "176dc175b78f56c0f321911d9c8eb2b77a78a4860b9c19db83835fea1a46649b"
 dependencies = [
- "cfg-if",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-deque"
-version = "0.8.3"
+version = "0.8.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef"
+checksum = "613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d"
 dependencies = [
- "cfg-if",
  "crossbeam-epoch",
  "crossbeam-utils",
 ]
 
 [[package]]
 name = "crossbeam-epoch"
-version = "0.9.15"
+version = "0.9.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7"
+checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e"
 dependencies = [
- "autocfg",
- "cfg-if",
  "crossbeam-utils",
- "memoffset",
- "scopeguard",
 ]
 
 [[package]]
 name = "crossbeam-utils"
-version = "0.8.16"
+version = "0.8.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294"
-dependencies = [
- "cfg-if",
-]
+checksum = "248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345"
 
 [[package]]
 name = "crypto-common"
@@ -1177,12 +1168,12 @@ dependencies = [
 
 [[package]]
 name = "darling"
-version = "0.20.3"
+version = "0.20.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0209d94da627ab5605dcccf08bb18afa5009cfbef48d8a8b7d7bdbc79be25c5e"
+checksum = "fc5d6b04b3fd0ba9926f945895de7d806260a2d7431ba82e7edaecb043c4c6b8"
 dependencies = [
- "darling_core 0.20.3",
- "darling_macro 0.20.3",
+ "darling_core 0.20.5",
+ "darling_macro 0.20.5",
 ]
 
 [[package]]
@@ -1201,9 +1192,9 @@ dependencies = [
 
 [[package]]
 name = "darling_core"
-version = "0.20.3"
+version = "0.20.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "177e3443818124b357d8e76f53be906d60937f0d3a90773a664fa63fa253e621"
+checksum = "04e48a959bcd5c761246f5d090ebc2fbf7b9cd527a492b07a67510c108f1e7e3"
 dependencies = [
  "fnv",
  "ident_case",
@@ -1226,23 +1217,22 @@ dependencies = [
 
 [[package]]
 name = "darling_macro"
-version = "0.20.3"
+version = "0.20.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "836a9bbc7ad63342d6d6e7b815ccab164bc77a2d95d84bc3117a8c0d5c98e2d5"
+checksum = "1d1545d67a2149e1d93b7e5c7752dce5a7426eb5d1357ddcfd89336b94444f77"
 dependencies = [
- "darling_core 0.20.3",
+ "darling_core 0.20.5",
  "quote",
  "syn 2.0.48",
 ]
 
 [[package]]
 name = "deranged"
-version = "0.3.9"
+version = "0.3.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0f32d04922c60427da6f9fef14d042d9edddef64cb9d4ce0d64d0685fbeb1fd3"
+checksum = "b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4"
 dependencies = [
  "powerfmt",
- "serde",
 ]
 
 [[package]]
@@ -1376,17 +1366,27 @@ dependencies = [
  "syn 2.0.48",
 ]
 
+[[package]]
+name = "env_filter"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a009aa4810eb158359dda09d0c87378e4bbb89b5a801f016885a4707ba24f7ea"
+dependencies = [
+ "log",
+ "regex",
+]
+
 [[package]]
 name = "env_logger"
-version = "0.10.2"
+version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580"
+checksum = "05e7cf40684ae96ade6232ed84582f40ce0a66efcd43a5117aef610534f8e0b8"
 dependencies = [
+ "anstream",
+ "anstyle",
+ "env_filter",
  "humantime",
- "is-terminal",
  "log",
- "regex",
- "termcolor",
 ]
 
 [[package]]
@@ -1422,9 +1422,9 @@ checksum = "0206175f82b8d6bf6652ff7d71a1e27fd2e4efde587fd368662814d6ec1d9ce0"
 
 [[package]]
 name = "event-listener"
-version = "4.0.0"
+version = "4.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "770d968249b5d99410d61f5bf89057f3199a077a04d087092f58e7d10692baae"
+checksum = "67b215c49b2b248c855fb73579eb1f4f26c38ffdc12973e20e07b91d78d5646e"
 dependencies = [
  "concurrent-queue",
  "parking",
@@ -1437,7 +1437,7 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "958e4d70b6d5e81971bebec42271ec641e7ff4e170a6fa605f2b8a8b65cb97d3"
 dependencies = [
- "event-listener 4.0.0",
+ "event-listener 4.0.3",
  "pin-project-lite",
 ]
 
@@ -1447,6 +1447,12 @@ version = "0.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4443176a9f2c162692bd3d352d745ef9413eec5782a80d8fd6f8a1ac692a07f7"
 
+[[package]]
+name = "fallible-iterator"
+version = "0.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2acce4a10f12dc2fb14a218589d4f1f62ef011b2d0cc4b3cb1bba8e94da14649"
+
 [[package]]
 name = "fallible-streaming-iterator"
 version = "0.1.9"
@@ -1582,14 +1588,13 @@ dependencies = [
 
 [[package]]
 name = "futures-lite"
-version = "2.0.1"
+version = "2.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d3831c2651acb5177cbd83943f3d9c8912c5ad03c76afcc0e9511ba568ec5ebb"
+checksum = "445ba825b27408685aaecefd65178908c36c6e96aaf6d8599419d46e624192ba"
 dependencies = [
  "fastrand 2.0.1",
  "futures-core",
  "futures-io",
- "memchr",
  "parking",
  "pin-project-lite",
 ]
@@ -1662,9 +1667,9 @@ dependencies = [
 
 [[package]]
 name = "getrandom"
-version = "0.2.11"
+version = "0.2.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fe9006bed769170c11f845cf00c7c1e9092aeb3f268e007c3e760ac68008070f"
+checksum = "190092ea657667030ac6a35e305e62fc4dd69fd98ac98631e5d3a2b1575a12b5"
 dependencies = [
  "cfg-if",
  "libc",
@@ -1719,7 +1724,7 @@ dependencies = [
  "futures-sink",
  "futures-util",
  "http",
- "indexmap 2.2.2",
+ "indexmap",
  "slab",
  "tokio",
  "tokio-util",
@@ -1741,7 +1746,7 @@ version = "0.14.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604"
 dependencies = [
- "ahash 0.8.6",
+ "ahash 0.8.7",
  "allocator-api2",
 ]
 
@@ -1762,9 +1767,9 @@ checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
 [[package]]
 name = "hermit-abi"
-version = "0.3.3"
+version = "0.3.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d77f7ec81a6d05a3abb01ab6eb7590f6083d08449fe5a1c8b1e620283546ccb7"
+checksum = "d0c62115964e08cb8039170eb33c1d0e2388a256930279edca206fff675f82c3"
 
 [[package]]
 name = "hex"
@@ -1774,9 +1779,9 @@ checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70"
 
 [[package]]
 name = "hgvs"
-version = "0.14.1"
+version = "0.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "92846aab72955dc5bd32092bc2eb2f1cfa8bd862f93ab2497cd60bae2d8cca36"
+checksum = "bdaf50d3b103c2ef84777dbc5e3796f335edc1ca7ebece6c2ac1c0f3e023d643"
 dependencies = [
  "base16ct",
  "bio",
@@ -1784,7 +1789,7 @@ dependencies = [
  "chrono",
  "enum-map",
  "flate2",
- "indexmap 2.2.2",
+ "indexmap",
  "lazy_static",
  "log",
  "md-5",
@@ -1810,11 +1815,11 @@ dependencies = [
 
 [[package]]
 name = "home"
-version = "0.5.5"
+version = "0.5.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5444c27eef6923071f7ebcc33e3444508466a76f7a2b93da00ed6e19f30c1ddb"
+checksum = "e3d1354bf6b7235cb4a0576c2619fd4ed18183f689b12b006a0ee7329eeff9a5"
 dependencies = [
- "windows-sys 0.48.0",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -1854,9 +1859,9 @@ checksum = "a17b27f28a7466846baca75f0a5244e546e44178eb7f1c07a3820f413e91c6b0"
 
 [[package]]
 name = "iana-time-zone"
-version = "0.1.58"
+version = "0.1.60"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8326b86b6cff230b97d0d312a6c40a60726df3332e721f72a1b035f451663b20"
+checksum = "e7ffbb5a1b541ea2561f8c41c087286cc091e21e556a4f09a8f6cbf17b69b141"
 dependencies = [
  "android_system_properties",
  "core-foundation-sys",
@@ -1891,17 +1896,6 @@ dependencies = [
  "unicode-normalization",
 ]
 
-[[package]]
-name = "indexmap"
-version = "1.9.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99"
-dependencies = [
- "autocfg",
- "hashbrown 0.12.3",
- "serde",
-]
-
 [[package]]
 name = "indexmap"
 version = "2.2.2"
@@ -1961,17 +1955,6 @@ dependencies = [
  "windows-sys 0.48.0",
 ]
 
-[[package]]
-name = "is-terminal"
-version = "0.4.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b"
-dependencies = [
- "hermit-abi",
- "rustix 0.38.26",
- "windows-sys 0.48.0",
-]
-
 [[package]]
 name = "itertools"
 version = "0.11.0"
@@ -1992,24 +1975,24 @@ dependencies = [
 
 [[package]]
 name = "itoa"
-version = "1.0.9"
+version = "1.0.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "af150ab688ff2122fcef229be89cb50dd66af9e01a4ff320cc137eecc9bacc38"
+checksum = "b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c"
 
 [[package]]
 name = "jobserver"
-version = "0.1.27"
+version = "0.1.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8c37f63953c4c63420ed5fd3d6d398c719489b9f872b9fa683262f8edd363c7d"
+checksum = "ab46a6e9526ddef3ae7f787c06f0f2600639ba80ea3eade3d8e670a2230f51d6"
 dependencies = [
  "libc",
 ]
 
 [[package]]
 name = "js-sys"
-version = "0.3.66"
+version = "0.3.68"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cee9c64da59eae3b50095c18d3e74f8b73c0b86d2792824ff01bbce68ba229ca"
+checksum = "406cda4b368d531c842222cf9d2600a9a4acce8d29423695379c6868a143a9ee"
 dependencies = [
  "wasm-bindgen",
 ]
@@ -2054,18 +2037,18 @@ checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55"
 
 [[package]]
 name = "libc"
-version = "0.2.150"
+version = "0.2.153"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "89d92a4743f9a61002fae18374ed11e7973f530cb3a3255fb354818118b2203c"
+checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
 
 [[package]]
 name = "libloading"
-version = "0.7.4"
+version = "0.8.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b67380fd3b2fbe7527a606e18729d21c6f3951633d0500574c4dc22d2d638b9f"
+checksum = "c571b676ddfc9a8c12f1f3d3085a7b163966a8fd8098a90640953ce5f6170161"
 dependencies = [
  "cfg-if",
- "winapi",
+ "windows-sys 0.48.0",
 ]
 
 [[package]]
@@ -2092,9 +2075,9 @@ dependencies = [
 
 [[package]]
 name = "libsqlite3-sys"
-version = "0.26.0"
+version = "0.27.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "afc22eff61b133b115c6e8c74e818c628d6d5e7a502afea6f64dee076dd94326"
+checksum = "cf4e226dcd58b4be396f7bd3c20da8fdee2911400705297ba7d2d7cc2c30f716"
 dependencies = [
  "pkg-config",
  "vcpkg",
@@ -2102,9 +2085,9 @@ dependencies = [
 
 [[package]]
 name = "libz-sys"
-version = "1.1.12"
+version = "1.1.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d97137b25e321a73eef1418d1d5d2eda4d77e12813f8e6dead84bc52c5870a7b"
+checksum = "037731f5d3aaa87a5675e895b63ddff1a87624bc29f77004ea829809654e48f6"
 dependencies = [
  "cc",
  "pkg-config",
@@ -2125,9 +2108,9 @@ checksum = "ef53942eb7bf7ff43a617b3e2c1c4a5ecf5944a7c1bc12d7ee39bbb15e5c1519"
 
 [[package]]
 name = "linux-raw-sys"
-version = "0.4.12"
+version = "0.4.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c4cd1a83af159aa67994778be9070f0ae1bd732942279cabb14f86f986a21456"
+checksum = "01cda141df6706de531b6c46c3a33ecca755538219bd484262fa09410c13539c"
 
 [[package]]
 name = "local-channel"
@@ -2229,19 +2212,19 @@ dependencies = [
  "futures",
  "hgvs",
  "hxdmp",
- "indexmap 2.2.2",
+ "indexmap",
  "indicatif",
  "insta",
  "jsonl",
  "lazy_static",
  "log",
  "nom",
- "noodles-bgzf 0.26.0",
- "noodles-core 0.14.0",
- "noodles-csi 0.30.0",
- "noodles-fasta 0.32.0",
- "noodles-tabix 0.36.0",
- "noodles-vcf 0.49.0",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
+ "noodles-fasta",
+ "noodles-tabix",
+ "noodles-vcf",
  "parse-display",
  "pbjson",
  "pbjson-build",
@@ -2275,18 +2258,9 @@ dependencies = [
 
 [[package]]
 name = "memchr"
-version = "2.6.4"
+version = "2.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f665ee40bc4a3c5590afb1e9677db74a508659dfd71e126420da8274909a0167"
-
-[[package]]
-name = "memoffset"
-version = "0.9.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c"
-dependencies = [
- "autocfg",
-]
+checksum = "523dc4f511e55ab87b694dc30d0f820d60906ef06413f93d4d7a1385599cc149"
 
 [[package]]
 name = "mime"
@@ -2302,18 +2276,18 @@ checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.1"
+version = "0.7.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7"
+checksum = "9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7"
 dependencies = [
  "adler",
 ]
 
 [[package]]
 name = "mio"
-version = "0.8.9"
+version = "0.8.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3dce281c5e46beae905d4de1870d8b1509a9142b62eedf18b443b011ca8343d0"
+checksum = "8f3d0b296e374a4e6f3c7b0a1f5a51d748a0d34c85e7dc48fc3fa9a87657fe09"
 dependencies = [
  "libc",
  "log",
@@ -2326,6 +2300,12 @@ name = "multimap"
 version = "0.8.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e5ce46fe64a9d73be07dcbe690a38ce1b293be448fd8ce1e6c1b8062c9f72c6a"
+
+[[package]]
+name = "multimap"
+version = "0.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e1a5d38b9b352dbd913288736af36af41c48d61b1a8cd34bcecd727561b7d511"
 dependencies = [
  "serde",
 ]
@@ -2393,23 +2373,11 @@ dependencies = [
 
 [[package]]
 name = "noodles-bed"
-version = "0.10.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "deba180b7b94c524307da91d5bc983e0ccb9a08c4e24384cc8f93e0210af254a"
-dependencies = [
- "noodles-core 0.12.0",
-]
-
-[[package]]
-name = "noodles-bgzf"
-version = "0.25.0"
+version = "0.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7d578e5a173cbfac77295db4188c959966ce24a3364e009d363170d1ed44066a"
+checksum = "c116ff14e3dd3ffa6c58771d1a2ee1205690e1c0fe78b0a3456402eebf44ad27"
 dependencies = [
- "byteorder",
- "bytes",
- "crossbeam-channel",
- "flate2",
+ "noodles-core",
 ]
 
 [[package]]
@@ -2428,31 +2396,12 @@ dependencies = [
  "tokio-util",
 ]
 
-[[package]]
-name = "noodles-core"
-version = "0.12.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "94fbe3192fe33acacabaedd387657f39b0fc606f1996d546db0dfe14703b843a"
-
 [[package]]
 name = "noodles-core"
 version = "0.14.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7336c3be652de4e05444c9b12a32331beb5ba3316e8872d92bfdd8ef3b06c282"
 
-[[package]]
-name = "noodles-csi"
-version = "0.28.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "912aaef460c3ccf466f79f681ed866c7e70b78da7af88c4bbb082a6a64971ebd"
-dependencies = [
- "bit-vec",
- "byteorder",
- "indexmap 2.2.2",
- "noodles-bgzf 0.25.0",
- "noodles-core 0.12.0",
-]
-
 [[package]]
 name = "noodles-csi"
 version = "0.30.0"
@@ -2461,21 +2410,9 @@ checksum = "a60dfe0919f7ecbd081a82eb1d32e8f89f9041932d035fe8309073c8c01277bf"
 dependencies = [
  "bit-vec",
  "byteorder",
- "indexmap 2.2.2",
- "noodles-bgzf 0.26.0",
- "noodles-core 0.14.0",
-]
-
-[[package]]
-name = "noodles-fasta"
-version = "0.30.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "310dcfb61e8e2cafb65d9da4b329a98a390f2b570c17599a7f4639328cfb3e2c"
-dependencies = [
- "bytes",
- "memchr",
- "noodles-bgzf 0.25.0",
- "noodles-core 0.12.0",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core",
 ]
 
 [[package]]
@@ -2486,37 +2423,23 @@ checksum = "ebb3e83e0f112d3482f5234a1eb219081f12cc3aab38a9eba00ef1846b43b63b"
 dependencies = [
  "bytes",
  "memchr",
- "noodles-bgzf 0.26.0",
- "noodles-core 0.14.0",
+ "noodles-bgzf",
+ "noodles-core",
 ]
 
 [[package]]
 name = "noodles-gff"
-version = "0.25.0"
+version = "0.27.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fec62bd9306cce6d551c9c7075beca940aec283efd18648b6d04860b693fd092"
+checksum = "14f8ec87fe3630f57d6d8ea24cbc2cbd0bfed1fe66238bda7a7c3fb6a36d3713"
 dependencies = [
- "indexmap 2.2.2",
- "noodles-bgzf 0.25.0",
- "noodles-core 0.12.0",
- "noodles-csi 0.28.0",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
  "percent-encoding",
 ]
 
-[[package]]
-name = "noodles-tabix"
-version = "0.34.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "63995f930f245b44f1a14d7e7571ce77111d2b88731d774ebeda951b726c8dfb"
-dependencies = [
- "bit-vec",
- "byteorder",
- "indexmap 2.2.2",
- "noodles-bgzf 0.25.0",
- "noodles-core 0.12.0",
- "noodles-csi 0.28.0",
-]
-
 [[package]]
 name = "noodles-tabix"
 version = "0.36.0"
@@ -2525,28 +2448,13 @@ checksum = "cc1ab29335a68d0c2bdf41460a67714ca69e23a1cbeb950ac5c38a9afa446a62"
 dependencies = [
  "bit-vec",
  "byteorder",
- "indexmap 2.2.2",
- "noodles-bgzf 0.26.0",
- "noodles-core 0.14.0",
- "noodles-csi 0.30.0",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
  "tokio",
 ]
 
-[[package]]
-name = "noodles-vcf"
-version = "0.47.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "610f14797affe3ecc3687732e310ff508c909dd18d3b12d0cd135bc4cc5593e9"
-dependencies = [
- "indexmap 2.2.2",
- "memchr",
- "noodles-bgzf 0.25.0",
- "noodles-core 0.12.0",
- "noodles-csi 0.28.0",
- "noodles-tabix 0.34.0",
- "percent-encoding",
-]
-
 [[package]]
 name = "noodles-vcf"
 version = "0.49.0"
@@ -2554,12 +2462,12 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2e1f2fa749afaccadc596ec55ccb7bdcd8101fa79f8382384223c0dbae3e245b"
 dependencies = [
  "futures",
- "indexmap 2.2.2",
+ "indexmap",
  "memchr",
- "noodles-bgzf 0.26.0",
- "noodles-core 0.14.0",
- "noodles-csi 0.30.0",
- "noodles-tabix 0.36.0",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
+ "noodles-tabix",
  "percent-encoding",
  "tokio",
 ]
@@ -2576,20 +2484,25 @@ dependencies = [
 
 [[package]]
 name = "num-complex"
-version = "0.4.4"
+version = "0.4.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1ba157ca0885411de85d6ca030ba7e2a83a28636056c7c699b07c8b6f7383214"
+checksum = "23c6602fda94a57c990fe0df199a035d83576b496aa29f4e634a8ac6004e68a6"
 dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "num-conv"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9"
+
 [[package]]
 name = "num-integer"
-version = "0.1.45"
+version = "0.1.46"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9"
+checksum = "7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f"
 dependencies = [
- "autocfg",
  "num-traits",
 ]
 
@@ -2606,9 +2519,9 @@ dependencies = [
 
 [[package]]
 name = "num-traits"
-version = "0.2.17"
+version = "0.2.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c"
+checksum = "da0df0e5185db44f69b44f26786fe401b6c293d1907744beaa7fa62b2e5a517a"
 dependencies = [
  "autocfg",
  "libm",
@@ -2632,18 +2545,18 @@ checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
 
 [[package]]
 name = "object"
-version = "0.32.1"
+version = "0.32.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9cf5f9dd3933bd50a9e1f149ec995f39ae2c496d31fd772c1fd45ebc27e902b0"
+checksum = "a6a622008b6e321afc04970976f62ee297fdbaa6f95318ca343e3eebb9648441"
 dependencies = [
  "memchr",
 ]
 
 [[package]]
 name = "once_cell"
-version = "1.18.0"
+version = "1.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d"
+checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
 
 [[package]]
 name = "ordered-float"
@@ -2776,7 +2689,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e1d3afd2628e69da2be385eb6f2fd57c8ac7977ceeff6dc166ff1657b0e386a9"
 dependencies = [
  "fixedbitset",
- "indexmap 2.2.2",
+ "indexmap",
 ]
 
 [[package]]
@@ -2822,9 +2735,9 @@ dependencies = [
 
 [[package]]
 name = "pkg-config"
-version = "0.3.27"
+version = "0.3.29"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964"
+checksum = "2900ede94e305130c13ddd391e0ab7cbaeb783945ae07a279c268cb05109c6cb"
 
 [[package]]
 name = "polling"
@@ -2844,23 +2757,23 @@ dependencies = [
 
 [[package]]
 name = "polling"
-version = "3.3.1"
+version = "3.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cf63fa624ab313c11656b4cda960bfc46c410187ad493c41f6ba2d8c1e991c9e"
+checksum = "30054e72317ab98eddd8561db0f6524df3367636884b7b21b703e4b280a84a14"
 dependencies = [
  "cfg-if",
  "concurrent-queue",
  "pin-project-lite",
- "rustix 0.38.26",
+ "rustix 0.38.31",
  "tracing",
  "windows-sys 0.52.0",
 ]
 
 [[package]]
 name = "portable-atomic"
-version = "1.5.1"
+version = "1.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3bccab0e7fd7cc19f820a1c8c91720af652d0c88dc9664dd72aef2614f04af3b"
+checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0"
 
 [[package]]
 name = "postgres"
@@ -2869,7 +2782,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7915b33ed60abc46040cbcaa25ffa1c7ec240668e0477c4f3070786f5916d451"
 dependencies = [
  "bytes",
- "fallible-iterator",
+ "fallible-iterator 0.2.0",
  "futures-util",
  "log",
  "tokio",
@@ -2885,7 +2798,7 @@ dependencies = [
  "base64",
  "byteorder",
  "bytes",
- "fallible-iterator",
+ "fallible-iterator 0.2.0",
  "hmac",
  "md-5",
  "memchr",
@@ -2902,7 +2815,7 @@ checksum = "8d2234cdee9408b523530a9b6d2d6b373d1db34f6a8e51dc03ded1828d7fb67c"
 dependencies = [
  "bytes",
  "chrono",
- "fallible-iterator",
+ "fallible-iterator 0.2.0",
  "postgres-protocol",
 ]
 
@@ -2930,9 +2843,9 @@ dependencies = [
 
 [[package]]
 name = "prettyplease"
-version = "0.2.15"
+version = "0.2.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae005bd773ab59b4725093fd7df83fd7892f7d8eafb48dbd7de6e024e4215f9d"
+checksum = "a41cf62165e97c7f814d2221421dbb9afcbcdb0a88068e5ea206e19951c2cbb5"
 dependencies = [
  "proc-macro2",
  "syn 2.0.48",
@@ -2986,13 +2899,13 @@ version = "0.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "731e0d9356b0c25f16f33b5be79b1c57b562f141ebfcdb0ad8ac2c13a24293b4"
 dependencies = [
- "bitflags 2.4.1",
+ "bitflags 2.4.2",
  "chrono",
  "flate2",
  "hex",
  "lazy_static",
  "procfs-core",
- "rustix 0.38.26",
+ "rustix 0.38.31",
 ]
 
 [[package]]
@@ -3001,7 +2914,7 @@ version = "0.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2d3554923a69f4ce04c4a754260c338f505ce22642d3830e049a399fc2059a29"
 dependencies = [
- "bitflags 2.4.1",
+ "bitflags 2.4.2",
  "chrono",
  "hex",
 ]
@@ -3026,7 +2939,7 @@ dependencies = [
  "heck",
  "itertools",
  "log",
- "multimap",
+ "multimap 0.8.3",
  "once_cell",
  "petgraph",
  "prettyplease",
@@ -3082,11 +2995,11 @@ dependencies = [
 
 [[package]]
 name = "quick_cache"
-version = "0.4.0"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f69f8d22fa3f34f3083d9a4375c038732c7a7e964de1beb81c544da92dfc40b8"
+checksum = "58c20af3800cee5134b79a3bd4a3d4b583c16ccfa5f53338f46400851a5b3819"
 dependencies = [
- "ahash 0.8.6",
+ "ahash 0.8.7",
  "equivalent",
  "hashbrown 0.14.3",
  "parking_lot",
@@ -3155,9 +3068,9 @@ checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
 
 [[package]]
 name = "rayon"
-version = "1.8.0"
+version = "1.8.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c27db03db7734835b3f53954b534c91069375ce6ccaa2e065441e07d9b6cdb1"
+checksum = "fa7237101a77a10773db45d62004a272517633fbcc3df19d96455ede1122e051"
 dependencies = [
  "either",
  "rayon-core",
@@ -3165,9 +3078,9 @@ dependencies = [
 
 [[package]]
 name = "rayon-core"
-version = "1.12.0"
+version = "1.12.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ce3fb6ad83f861aac485e76e1985cd109d9a3713802152be56c3b1f0e0658ed"
+checksum = "1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2"
 dependencies = [
  "crossbeam-deque",
  "crossbeam-utils",
@@ -3228,24 +3141,24 @@ checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f"
 
 [[package]]
 name = "relative-path"
-version = "1.9.0"
+version = "1.9.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c707298afce11da2efef2f600116fa93ffa7a032b5d7b628aa17711ec81383ca"
+checksum = "e898588f33fdd5b9420719948f9f2a32c922a246964576f71ba7f24f80610fbc"
 
 [[package]]
 name = "rend"
-version = "0.4.1"
+version = "0.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a2571463863a6bd50c32f94402933f03457a3fbaf697a707c5be741e459f08fd"
+checksum = "71fe3824f5629716b1589be05dacd749f6aa084c87e00e016714a8cdfccc997c"
 dependencies = [
  "bytecheck",
 ]
 
 [[package]]
 name = "rkyv"
-version = "0.7.43"
+version = "0.7.44"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "527a97cdfef66f65998b5f3b637c26f5a5ec09cc52a3f9932313ac645f4190f5"
+checksum = "5cba464629b3394fc4dbc6f940ff8f5b4ff5c7aef40f29166fd4ad12acbc99c0"
 dependencies = [
  "bitvec",
  "bytecheck",
@@ -3261,9 +3174,9 @@ dependencies = [
 
 [[package]]
 name = "rkyv_derive"
-version = "0.7.43"
+version = "0.7.44"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b5c462a1328c8e67e4d6dbad1eb0355dd43e8ab432c6e227a43657f16ade5033"
+checksum = "a7dddfff8de25e6f62b9d64e6e432bf1c6736c57d20323e15ee10435fbda7c65"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -3322,12 +3235,12 @@ dependencies = [
 
 [[package]]
 name = "rusqlite"
-version = "0.29.0"
+version = "0.30.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "549b9d036d571d42e6e85d1c1425e2ac83491075078ca9a15be021c56b1641f2"
+checksum = "a78046161564f5e7cd9008aff3b2990b3850dc8e0349119b98e8f251e099f24d"
 dependencies = [
- "bitflags 2.4.1",
- "fallible-iterator",
+ "bitflags 2.4.2",
+ "fallible-iterator 0.3.0",
  "fallible-streaming-iterator",
  "hashlink",
  "libsqlite3-sys",
@@ -3336,9 +3249,9 @@ dependencies = [
 
 [[package]]
 name = "rust_decimal"
-version = "1.33.1"
+version = "1.34.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "06676aec5ccb8fc1da723cc8c0f9a46549f21ebb8753d3915c6c41db1e7f1dc4"
+checksum = "755392e1a2f77afd95580d3f0d0e94ac83eeeb7167552c9b5bca549e61a94d83"
 dependencies = [
  "arrayvec",
  "borsh",
@@ -3377,7 +3290,7 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366"
 dependencies = [
- "semver 1.0.20",
+ "semver 1.0.21",
 ]
 
 [[package]]
@@ -3396,14 +3309,14 @@ dependencies = [
 
 [[package]]
 name = "rustix"
-version = "0.38.26"
+version = "0.38.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9470c4bf8246c8daf25f9598dca807fb6510347b1e1cfa55749113850c79d88a"
+checksum = "6ea3e1a662af26cd7a3ba09c0297a31af215563ecf42817c98df621387f4e949"
 dependencies = [
- "bitflags 2.4.1",
+ "bitflags 2.4.2",
  "errno",
  "libc",
- "linux-raw-sys 0.4.12",
+ "linux-raw-sys 0.4.13",
  "windows-sys 0.52.0",
 ]
 
@@ -3415,9 +3328,9 @@ checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4"
 
 [[package]]
 name = "ryu"
-version = "1.0.15"
+version = "1.0.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1ad4cc8da4ef723ed60bced201181d83791ad433213d8c24efffda1eec85d741"
+checksum = "f98d2aa92eebf49b69786be48e4477826b256916e84a57ff2a4f21923b48eb4c"
 
 [[package]]
 name = "safe_arch"
@@ -3448,20 +3361,20 @@ checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
 [[package]]
 name = "semver"
-version = "1.0.20"
+version = "1.0.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "836fa6a3e1e547f9a2c4040802ec865b5d85f4014efe00555d7090a3dcaa1090"
+checksum = "b97ed7a9823b74f99c7742f5336af7be5ecd3eeafcb1507d1fa93347b1d589b0"
 
 [[package]]
 name = "seqrepo"
-version = "0.9.0"
+version = "0.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f2952aee50ad05e57127f0857aa9553bbce29aea59817da2127c34ce09f6dd65"
+checksum = "88f98fe096b30d454f0dc995ad206d67356ea23292128380252f8d76b62d4c17"
 dependencies = [
  "chrono",
- "noodles-bgzf 0.25.0",
- "noodles-core 0.12.0",
- "noodles-fasta 0.30.0",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-fasta",
  "rusqlite",
  "thiserror",
  "tracing",
@@ -3469,18 +3382,18 @@ dependencies = [
 
 [[package]]
 name = "serde"
-version = "1.0.195"
+version = "1.0.196"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "63261df402c67811e9ac6def069e4786148c4563f4b50fd4bf30aa370d626b02"
+checksum = "870026e60fa08c69f064aa766c10f10b1d62db9ccd4d0abb206472bee0ce3b32"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.195"
+version = "1.0.196"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46fe8f8603d81ba86327b23a2e9cdf49e1255fb94a4c5f297f6ee0547178ea2c"
+checksum = "33c85360c95e7d137454dc81d9a4ed2b8efd8fbe19cee57357b32b9771fccb67"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -3489,11 +3402,11 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.111"
+version = "1.0.113"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "176e46fa42316f18edd598015a5166857fc835ec732f5215eac6b7bdbf0a84f4"
+checksum = "69801b70b1c3dac963ecb03a364ba0ceda9cf60c71cfe475e99864759c8b8a79"
 dependencies = [
- "indexmap 2.2.2",
+ "indexmap",
  "itoa",
  "ryu",
  "serde",
@@ -3513,15 +3426,14 @@ dependencies = [
 
 [[package]]
 name = "serde_with"
-version = "3.5.1"
+version = "3.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f5c9fdb6b00a489875b22efd4b78fe2b363b72265cc5f6eb2e2b9ee270e6140c"
+checksum = "1b0ed1662c5a68664f45b76d18deb0e234aff37207086803165c961eb695e981"
 dependencies = [
  "base64",
  "chrono",
  "hex",
- "indexmap 1.9.3",
- "indexmap 2.2.2",
+ "indexmap",
  "serde",
  "serde_json",
  "serde_with_macros",
@@ -3530,11 +3442,11 @@ dependencies = [
 
 [[package]]
 name = "serde_with_macros"
-version = "3.5.1"
+version = "3.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dbff351eb4b33600a2e138dfa0b10b65a238ea8ff8fb2387c422c5022a3e8298"
+checksum = "568577ff0ef47b879f736cd66740e022f3672788cdf002a05a4e609ea5a6fb15"
 dependencies = [
- "darling 0.20.3",
+ "darling 0.20.5",
  "proc-macro2",
  "quote",
  "syn 2.0.48",
@@ -3542,11 +3454,11 @@ dependencies = [
 
 [[package]]
 name = "serde_yaml"
-version = "0.9.30"
+version = "0.9.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b1bf28c79a99f70ee1f1d83d10c875d2e70618417fda01ad1785e027579d9d38"
+checksum = "adf8a49373e98a4c5f0ceb5d05aa7c648d75f63774981ed95b7c7443bbd50c6e"
 dependencies = [
- "indexmap 2.2.2",
+ "indexmap",
  "itoa",
  "ryu",
  "serde",
@@ -3620,9 +3532,9 @@ checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a"
 
 [[package]]
 name = "similar"
-version = "2.3.0"
+version = "2.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2aeaf503862c419d66959f5d7ca015337d864e9c49485d771b732e2a20453597"
+checksum = "32fea41aca09ee824cc9724996433064c89f7777e60762749a4170a14abbfa21"
 
 [[package]]
 name = "siphasher"
@@ -3641,9 +3553,9 @@ dependencies = [
 
 [[package]]
 name = "smallvec"
-version = "1.11.2"
+version = "1.13.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4dccd0940a2dcdf68d092b8cbab7dc0ad8fa938bf95787e1b916b0e3d0e8e970"
+checksum = "e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7"
 
 [[package]]
 name = "socket2"
@@ -3723,9 +3635,6 @@ name = "strum"
 version = "0.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "290d54ea6f91c969195bdbcd7442c8c2a2ba87da8bf60a7ee86a235d4bc1e125"
-dependencies = [
- "strum_macros 0.25.3",
-]
 
 [[package]]
 name = "strum"
@@ -3816,40 +3725,30 @@ checksum = "921f1e9c427802414907a48b21a6504ff6b3a15a1a3cf37e699590949ad9befc"
 
 [[package]]
 name = "tempfile"
-version = "3.9.0"
+version = "3.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "01ce4141aa927a6d1bd34a041795abd0db1cccba5d5f24b009f694bdf3a1f3fa"
+checksum = "a365e8cd18e44762ef95d87f284f4b5cd04107fec2ff3052bd6a3e6069669e67"
 dependencies = [
  "cfg-if",
  "fastrand 2.0.1",
- "redox_syscall",
- "rustix 0.38.26",
+ "rustix 0.38.31",
  "windows-sys 0.52.0",
 ]
 
-[[package]]
-name = "termcolor"
-version = "1.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ff1bc3d3f05aff0403e8ac0d92ced918ec05b666a43f83297ccef5bea8a3d449"
-dependencies = [
- "winapi-util",
-]
-
 [[package]]
 name = "thiserror"
-version = "1.0.50"
+version = "1.0.56"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f9a7210f5c9a7156bb50aa36aed4c95afb51df0df00713949448cf9e97d382d2"
+checksum = "d54378c645627613241d077a3a79db965db602882668f9136ac42af9ecb730ad"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.50"
+version = "1.0.56"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "266b2e40bc00e5a6c09c3584011e08b06f123c00362c92b975ba9843aaaa14b8"
+checksum = "fa0faa943b50f3db30a20aa7e265dbc66076993efed8463e8de414e5d06d3471"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -3874,12 +3773,13 @@ dependencies = [
 
 [[package]]
 name = "time"
-version = "0.3.30"
+version = "0.3.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c4a34ab300f2dee6e562c10a046fc05e358b29f9bf92277f30c3c8d82275f6f5"
+checksum = "c8248b6521bb14bc45b4067159b9b6ad792e2d6d754d6c41fb50e29fefe38749"
 dependencies = [
  "deranged",
  "itoa",
+ "num-conv",
  "powerfmt",
  "serde",
  "time-core",
@@ -3894,10 +3794,11 @@ checksum = "ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3"
 
 [[package]]
 name = "time-macros"
-version = "0.2.15"
+version = "0.2.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4ad70d68dba9e1f8aceda7aa6711965dfec1cac869f311a51bd08b3a2ccbce20"
+checksum = "7ba3a3ef41e6672a2f0f001392bb5dcd3ff0a9992d618ca761a11c3121547774"
 dependencies = [
+ "num-conv",
  "time-core",
 ]
 
@@ -3918,9 +3819,9 @@ checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
 
 [[package]]
 name = "tokio"
-version = "1.35.1"
+version = "1.36.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c89b4efa943be685f629b149f53829423f8f5531ea21249408e8e2f8671ec104"
+checksum = "61285f6515fa018fb2d1e46eb21223fff441ee8db5d0f1435e8ab4f5cdb80931"
 dependencies = [
  "backtrace",
  "bytes",
@@ -3955,7 +3856,7 @@ dependencies = [
  "async-trait",
  "byteorder",
  "bytes",
- "fallible-iterator",
+ "fallible-iterator 0.2.0",
  "futures-channel",
  "futures-util",
  "log",
@@ -3994,11 +3895,11 @@ checksum = "3550f4e9685620ac18a50ed434eb3aec30db8ba93b0287467bca5826ea25baf1"
 
 [[package]]
 name = "toml_edit"
-version = "0.21.0"
+version = "0.21.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d34d383cd00a163b4a5b85053df514d45bc330f6de7737edfe0a93311d1eaa03"
+checksum = "6a8534fd7f78b5405e860340ad6575217ce99f38d4d5c8f2442cb5ecb50090e1"
 dependencies = [
- "indexmap 2.2.2",
+ "indexmap",
  "toml_datetime",
  "winnow",
 ]
@@ -4102,9 +4003,9 @@ checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
 
 [[package]]
 name = "unicode-bidi"
-version = "0.3.13"
+version = "0.3.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460"
+checksum = "08f95100a766bf4f8f28f90d77e0a5461bbdb219042e7679bebe79004fed8d75"
 
 [[package]]
 name = "unicode-ident"
@@ -4175,9 +4076,9 @@ checksum = "830b7e5d4d90034032940e4ace0d9a9a057e7a45cd94e6c007832e39edb82f6d"
 
 [[package]]
 name = "value-bag"
-version = "1.4.2"
+version = "1.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4a72e1902dde2bd6441347de2b70b7f5d59bf157c6c62f0c44572607a1d55bbe"
+checksum = "126e423afe2dd9ac52142e7e9d5ce4135d7e13776c529d27fd6bc49f19e3280b"
 
 [[package]]
 name = "vcpkg"
@@ -4214,9 +4115,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wasm-bindgen"
-version = "0.2.89"
+version = "0.2.91"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0ed0d4f68a3015cc185aff4db9506a015f4b96f95303897bfa23f846db54064e"
+checksum = "c1e124130aee3fb58c5bdd6b639a0509486b0338acaaae0c84a5124b0f588b7f"
 dependencies = [
  "cfg-if",
  "wasm-bindgen-macro",
@@ -4224,9 +4125,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-backend"
-version = "0.2.89"
+version = "0.2.91"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1b56f625e64f3a1084ded111c4d5f477df9f8c92df113852fa5a374dbda78826"
+checksum = "c9e7e1900c352b609c8488ad12639a311045f40a35491fb69ba8c12f758af70b"
 dependencies = [
  "bumpalo",
  "log",
@@ -4239,9 +4140,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-futures"
-version = "0.4.39"
+version = "0.4.41"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac36a15a220124ac510204aec1c3e5db8a22ab06fd6706d881dc6149f8ed9a12"
+checksum = "877b9c3f61ceea0e56331985743b13f3d25c406a7098d45180fb5f09bc19ed97"
 dependencies = [
  "cfg-if",
  "js-sys",
@@ -4251,9 +4152,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro"
-version = "0.2.89"
+version = "0.2.91"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0162dbf37223cd2afce98f3d0785506dcb8d266223983e4b5b525859e6e182b2"
+checksum = "b30af9e2d358182b5c7449424f017eba305ed32a7010509ede96cdc4696c46ed"
 dependencies = [
  "quote",
  "wasm-bindgen-macro-support",
@@ -4261,9 +4162,9 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-macro-support"
-version = "0.2.89"
+version = "0.2.91"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f0eb82fcb7930ae6219a7ecfd55b217f5f0893484b7a13022ebb2b2bf20b5283"
+checksum = "642f325be6301eb8107a83d12a8ac6c1e1c54345a7ef1a9261962dfefda09e66"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -4274,15 +4175,15 @@ dependencies = [
 
 [[package]]
 name = "wasm-bindgen-shared"
-version = "0.2.89"
+version = "0.2.91"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ab9b36309365056cd639da3134bf87fa8f3d86008abf99e612384a6eecd459f"
+checksum = "4f186bd2dcf04330886ce82d6f33dd75a7bfcf69ecf5763b89fcde53b6ac9838"
 
 [[package]]
 name = "web-sys"
-version = "0.3.66"
+version = "0.3.68"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "50c24a44ec86bb68fbecd1b3efed7e85ea5621b39b35ef2766b66cd984f8010f"
+checksum = "96565907687f7aceb35bc5fc03770a8a0471d82e479f25832f54a0e3f4b28446"
 dependencies = [
  "js-sys",
  "wasm-bindgen",
@@ -4297,7 +4198,7 @@ dependencies = [
  "either",
  "home",
  "once_cell",
- "rustix 0.38.26",
+ "rustix 0.38.31",
 ]
 
 [[package]]
@@ -4312,9 +4213,9 @@ dependencies = [
 
 [[package]]
 name = "wide"
-version = "0.7.13"
+version = "0.7.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c68938b57b33da363195412cfc5fc37c9ed49aa9cfe2156fde64b8d2c9498242"
+checksum = "89beec544f246e679fc25490e3f8e08003bc4bf612068f325120dad4cea02c1c"
 dependencies = [
  "bytemuck",
  "safe_arch",
@@ -4336,15 +4237,6 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
 
-[[package]]
-name = "winapi-util"
-version = "0.1.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596"
-dependencies = [
- "winapi",
-]
-
 [[package]]
 name = "winapi-x86_64-pc-windows-gnu"
 version = "0.4.0"
@@ -4353,20 +4245,11 @@ checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
 
 [[package]]
 name = "windows-core"
-version = "0.51.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1f8cf84f35d2db49a46868f947758c7a1138116f7fac3bc844f43ade1292e64"
-dependencies = [
- "windows-targets 0.48.5",
-]
-
-[[package]]
-name = "windows-sys"
-version = "0.45.0"
+version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0"
+checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
 dependencies = [
- "windows-targets 0.42.2",
+ "windows-targets 0.52.0",
 ]
 
 [[package]]
@@ -4387,21 +4270,6 @@ dependencies = [
  "windows-targets 0.52.0",
 ]
 
-[[package]]
-name = "windows-targets"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071"
-dependencies = [
- "windows_aarch64_gnullvm 0.42.2",
- "windows_aarch64_msvc 0.42.2",
- "windows_i686_gnu 0.42.2",
- "windows_i686_msvc 0.42.2",
- "windows_x86_64_gnu 0.42.2",
- "windows_x86_64_gnullvm 0.42.2",
- "windows_x86_64_msvc 0.42.2",
-]
-
 [[package]]
 name = "windows-targets"
 version = "0.48.5"
@@ -4432,12 +4300,6 @@ dependencies = [
  "windows_x86_64_msvc 0.52.0",
 ]
 
-[[package]]
-name = "windows_aarch64_gnullvm"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8"
-
 [[package]]
 name = "windows_aarch64_gnullvm"
 version = "0.48.5"
@@ -4450,12 +4312,6 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "cb7764e35d4db8a7921e09562a0304bf2f93e0a51bfccee0bd0bb0b666b015ea"
 
-[[package]]
-name = "windows_aarch64_msvc"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43"
-
 [[package]]
 name = "windows_aarch64_msvc"
 version = "0.48.5"
@@ -4468,12 +4324,6 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bbaa0368d4f1d2aaefc55b6fcfee13f41544ddf36801e793edbbfd7d7df075ef"
 
-[[package]]
-name = "windows_i686_gnu"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f"
-
 [[package]]
 name = "windows_i686_gnu"
 version = "0.48.5"
@@ -4486,12 +4336,6 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a28637cb1fa3560a16915793afb20081aba2c92ee8af57b4d5f28e4b3e7df313"
 
-[[package]]
-name = "windows_i686_msvc"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060"
-
 [[package]]
 name = "windows_i686_msvc"
 version = "0.48.5"
@@ -4504,12 +4348,6 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ffe5e8e31046ce6230cc7215707b816e339ff4d4d67c65dffa206fd0f7aa7b9a"
 
-[[package]]
-name = "windows_x86_64_gnu"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36"
-
 [[package]]
 name = "windows_x86_64_gnu"
 version = "0.48.5"
@@ -4522,12 +4360,6 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3d6fa32db2bc4a2f5abeacf2b69f7992cd09dca97498da74a151a3132c26befd"
 
-[[package]]
-name = "windows_x86_64_gnullvm"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3"
-
 [[package]]
 name = "windows_x86_64_gnullvm"
 version = "0.48.5"
@@ -4540,12 +4372,6 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e"
 
-[[package]]
-name = "windows_x86_64_msvc"
-version = "0.42.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0"
-
 [[package]]
 name = "windows_x86_64_msvc"
 version = "0.48.5"
@@ -4560,9 +4386,9 @@ checksum = "dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04"
 
 [[package]]
 name = "winnow"
-version = "0.5.35"
+version = "0.5.39"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1931d78a9c73861da0134f453bb1f790ce49b2e30eba8410b4b79bac72b46a2d"
+checksum = "5389a154b01683d28c77f8f68f49dea75f0a4da32557a58f68ee51ebba472d29"
 dependencies = [
  "memchr",
 ]
@@ -4593,18 +4419,18 @@ checksum = "09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec"
 
 [[package]]
 name = "zerocopy"
-version = "0.7.31"
+version = "0.7.32"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1c4061bedbb353041c12f413700357bec76df2c7e2ca8e4df8bac24c6bf68e3d"
+checksum = "74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be"
 dependencies = [
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.7.31"
+version = "0.7.32"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b3c129550b3e6de3fd0ba67ba5c81818f9805e58b8d7fee80a3a59d2c9fc601a"
+checksum = "9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6"
 dependencies = [
  "proc-macro2",
  "quote",
diff --git a/Cargo.toml b/Cargo.toml
index c3cd9baa..7aeed110 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -27,7 +27,7 @@ path = "src/main.rs"
 
 [dependencies]
 actix-web = "4.5"
-annonars = "0.34"
+annonars = "0.35"
 anyhow = "1.0"
 async-compression = { version = "0.4", features = ["tokio", "gzip"] }
 bgzip = "0.3"
@@ -41,10 +41,10 @@ clap = { version = "4.4", features = ["derive"] }
 csv = "1.3"
 derivative = "2.2"
 derive_builder = { version = "0.13", features = ["clippy"] }
-env_logger = "0.10"
+env_logger = "0.11"
 flate2 = "1.0"
 futures = "0.3"
-hgvs = "0.14.0"
+hgvs = "0.15"
 indexmap = { version = "2.2", features = ["serde"] }
 indicatif = "0.17"
 jsonl = "4.0"
@@ -65,10 +65,10 @@ rand = "0.8"
 rand_core = "0.6"
 rocksdb = { version = "0.21", features = ["multi-threaded-cf"] }
 rustc-hash = "1.1"
-seqrepo = "0.9"
+seqrepo = "0.10"
 serde_json = "1.0"
 serde = { version = "1.0", features = ["derive"] }
-serde_with = { version = "3.5", features = ["indexmap_2"] }
+serde_with = { version = "3.6", features=["alloc", "macros", "indexmap_2"], default-features = false }
 serde_yaml = "0.9"
 strum = { version = "0.26", features = ["derive"] }
 tempfile = "3"
@@ -78,8 +78,8 @@ tracing-subscriber = "0.3"
 tracing = { version = "0.1", features = ["log"] }
 uuid = { version = "1.7", features = ["fast-rng", "serde"] }
 zstd = "0.13"
-pbjson = "0.6.0"
-pbjson-types = "0.6.0"
+pbjson = "0.6"
+pbjson-types = "0.6"
 
 [build-dependencies]
 anyhow = "1.0"
diff --git a/fixit.sh b/fixit.sh
new file mode 100644
index 00000000..0a56d48b
--- /dev/null
+++ b/fixit.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/bash
+
+set -euo pipefail
+set -x
+
+for s in $(find . -name 'bootstrap.sh' | sort); do
+    bash $s
+done