From db5be40076699a5e9d56f1609bdfc88aef3d54f4 Mon Sep 17 00:00:00 2001
From: "J. Christian Heide" <christian_heide@eva.mpg.de>
Date: Wed, 18 Oct 2023 14:32:47 +0200
Subject: [PATCH] Update dependencies

---
 Cargo.lock | 167 ++++++++++++++++++++++++++---------------------------
 Cargo.toml |   2 +-
 2 files changed, 84 insertions(+), 85 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index e2c6e97..25c2477 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -10,9 +10,9 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
 
 [[package]]
 name = "aho-corasick"
-version = "1.1.1"
+version = "1.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ea5d730647d4fadd988536d06fecce94b7b4f2a7efdae548f1cf4b63205518ab"
+checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0"
 dependencies = [
  "memchr",
 ]
@@ -182,9 +182,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
 
 [[package]]
 name = "bitflags"
-version = "2.4.0"
+version = "2.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b4682ae6287fcf752ecaabbfcc7b6f9b72aa33933dc23a554d853aea8eea8635"
+checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07"
 
 [[package]]
 name = "block-buffer"
@@ -197,9 +197,9 @@ dependencies = [
 
 [[package]]
 name = "built"
-version = "0.7.0"
+version = "0.7.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1462f4ab147e1378c64dacd28f03a56d4771d93eab6c325265a35355ce47213d"
+checksum = "38d17f4d6e4dc36d1a02fbedc2753a096848e7c1b0772f7654eab8e2c927dd53"
 dependencies = [
  "git2",
 ]
@@ -234,9 +234,9 @@ checksum = "374d28ec25809ee0e23827c2ab573d729e293f281dfe393500e7ad618baa61c6"
 
 [[package]]
 name = "byteorder"
-version = "1.4.3"
+version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610"
+checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "bytes"
@@ -485,9 +485,12 @@ checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
 
 [[package]]
 name = "deranged"
-version = "0.3.8"
+version = "0.3.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f2696e8a945f658fd14dc3b87242e6b80cd0f36ff04ea560fa39082368847946"
+checksum = "0f32d04922c60427da6f9fef14d042d9edddef64cb9d4ce0d64d0685fbeb1fd3"
+dependencies = [
+ "powerfmt",
+]
 
 [[package]]
 name = "derive-new"
@@ -550,25 +553,14 @@ checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
 
 [[package]]
 name = "errno"
-version = "0.3.4"
+version = "0.3.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "add4f07d43996f76ef320709726a556a9d4f965d9410d8d0271132d2f8293480"
+checksum = "ac3e13f66a2f95e32a39eaa81f6b95d42878ca0e1db0c7543723dfe12557e860"
 dependencies = [
- "errno-dragonfly",
  "libc",
  "windows-sys 0.48.0",
 ]
 
-[[package]]
-name = "errno-dragonfly"
-version = "0.1.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf"
-dependencies = [
- "cc",
- "libc",
-]
-
 [[package]]
 name = "fastrand"
 version = "2.0.1"
@@ -589,9 +581,9 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80"
 
 [[package]]
 name = "flate2"
-version = "1.0.27"
+version = "1.0.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c6c98ee8095e9d1dcbf2fcc6d95acccb90d1c81db1e44725c6a984b1dbdfb010"
+checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e"
 dependencies = [
  "crc32fast",
  "miniz_oxide",
@@ -654,7 +646,7 @@ version = "0.18.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "fbf97ba92db08df386e10c8ede66a2a0369bd277090afd8710e19e38de9ec0cd"
 dependencies = [
- "bitflags 2.4.0",
+ "bitflags 2.4.1",
  "libc",
  "libgit2-sys",
  "log",
@@ -751,9 +743,9 @@ checksum = "af150ab688ff2122fcef229be89cb50dd66af9e01a4ff320cc137eecc9bacc38"
 
 [[package]]
 name = "jobserver"
-version = "0.1.26"
+version = "0.1.27"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "936cfd212a0155903bcbc060e316fb6cc7cbf2e1907329391ebadc1fe0ce77c2"
+checksum = "8c37f63953c4c63420ed5fd3d6d398c719489b9f872b9fa683262f8edd363c7d"
 dependencies = [
  "libc",
 ]
@@ -839,9 +831,9 @@ dependencies = [
 
 [[package]]
 name = "libc"
-version = "0.2.148"
+version = "0.2.149"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9cdc71e17332e86d2e1d38c1f99edcb6288ee11b815fb1a4b049eaa2114d369b"
+checksum = "a08173bc88b7955d1b3145aa561539096c421ac8debde8cbc3612ec635fee29b"
 
 [[package]]
 name = "libgit2-sys"
@@ -857,9 +849,9 @@ dependencies = [
 
 [[package]]
 name = "libm"
-version = "0.2.7"
+version = "0.2.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f7012b1bbb0719e1097c47611d3898568c546d597c2e74d66f6087edd5233ff4"
+checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
 [[package]]
 name = "libmimalloc-sys"
@@ -885,9 +877,9 @@ dependencies = [
 
 [[package]]
 name = "linux-raw-sys"
-version = "0.4.8"
+version = "0.4.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3852614a3bd9ca9804678ba6be5e3b8ce76dfc902cae004e3e0c44051b6e88db"
+checksum = "da2479e8c062e40bf0066ffa0bc823de0a9368974af99c9f6df941d2c231e03f"
 
 [[package]]
 name = "log"
@@ -1067,9 +1059,9 @@ dependencies = [
 
 [[package]]
 name = "noodles"
-version = "0.52.0"
+version = "0.53.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72a89dc73b84e008ea54345c0f32b4500364694fdb052589423bcd6d8bae1db2"
+checksum = "827deee2dbf244a3bd55e5e0ecdd5abc29f8afc9f5a0dc837019a5b5a261f6b6"
 dependencies = [
  "noodles-bam",
  "noodles-bgzf",
@@ -1082,9 +1074,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-bam"
-version = "0.46.0"
+version = "0.47.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "498392f7b8443450ecded1d213a69d0408aae89e63e372ffd11a24ab4ddadd7f"
+checksum = "b2c7e7720ce90614c24855d8eca85f97295af796497bb733ace6e1e085e1c45b"
 dependencies = [
  "bit-vec",
  "byteorder",
@@ -1097,9 +1089,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-bgzf"
-version = "0.24.0"
+version = "0.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8f4c43ff0879c542c1d8fd570c03e368f629587721d10267f2619e36afc9c9b0"
+checksum = "7d578e5a173cbfac77295db4188c959966ce24a3364e009d363170d1ed44066a"
 dependencies = [
  "byteorder",
  "bytes",
@@ -1115,11 +1107,11 @@ checksum = "94fbe3192fe33acacabaedd387657f39b0fc606f1996d546db0dfe14703b843a"
 
 [[package]]
 name = "noodles-cram"
-version = "0.43.0"
+version = "0.44.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "26608626412c3ed0f61efb24af5ba8d8867a1414f0fbc19b5f251188c918360d"
+checksum = "7aea10ef8984fb1f5edf165cc1a4295b284fadb87076086d74399468327ea2b5"
 dependencies = [
- "bitflags 2.4.0",
+ "bitflags 2.4.1",
  "byteorder",
  "bytes",
  "bzip2",
@@ -1134,9 +1126,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-csi"
-version = "0.24.0"
+version = "0.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1b2bb780250c88bc9ea69b56c1aa9df75decc6b79035f3f5ab10c0cd84d24fc6"
+checksum = "f327250086b20edade50756b6aee1851d656a3a5967cf94cbe4d4e10a5ef85d7"
 dependencies = [
  "bit-vec",
  "byteorder",
@@ -1147,9 +1139,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-fasta"
-version = "0.29.0"
+version = "0.30.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1012431f881aad1912f9650a8d33e7f7493c6202bc2e889949ec1bc26a55f26d"
+checksum = "310dcfb61e8e2cafb65d9da4b329a98a390f2b570c17599a7f4639328cfb3e2c"
 dependencies = [
  "bytes",
  "memchr",
@@ -1159,20 +1151,20 @@ dependencies = [
 
 [[package]]
 name = "noodles-fastq"
-version = "0.8.0"
+version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e1763486d2d1a1e39a86676a47aa05728c75f73f0f883415e36439711ead2641"
+checksum = "76634b8ebcf78854bf48e4551a9484539a83ee0449acbd6308083c63a2a91dee"
 dependencies = [
  "memchr",
 ]
 
 [[package]]
 name = "noodles-sam"
-version = "0.43.0"
+version = "0.44.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3520332ff9823a7afc306e3871d70b29ec2f6ce8546664579ddab1d154ac6ac2"
+checksum = "9295b6c8424bde6ef7093e404499133185a23c8559b22c4892fa876a415cc5ec"
 dependencies = [
- "bitflags 2.4.0",
+ "bitflags 2.4.1",
  "indexmap",
  "lexical-core",
  "memchr",
@@ -1213,9 +1205,9 @@ dependencies = [
 
 [[package]]
 name = "num-traits"
-version = "0.2.16"
+version = "0.2.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f30b0abd723be7e2ffca1272140fac1a2f084c77ec3e123c192b66af1ee9e6c2"
+checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c"
 dependencies = [
  "autocfg",
  "libm",
@@ -1244,9 +1236,9 @@ checksum = "0ab1bc2a289d34bd04a330323ac98a1b4bc82c9d9fcb1e66b63caa84da26b575"
 
 [[package]]
 name = "ordered-float"
-version = "3.9.1"
+version = "3.9.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2a54938017eacd63036332b4ae5c8a49fc8c0c1d6d629893057e4f13609edd06"
+checksum = "f1e1c390732d15f1d48471625cd92d154e66db2c56645e29a9cd26f4699f72dc"
 dependencies = [
  "num-traits",
 ]
@@ -1307,6 +1299,12 @@ dependencies = [
  "plotters-backend",
 ]
 
+[[package]]
+name = "powerfmt"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391"
+
 [[package]]
 name = "ppv-lite86"
 version = "0.2.17"
@@ -1339,9 +1337,9 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.67"
+version = "1.0.69"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3d433d9f1a3e8c1263d9456598b16fec66f4acc9a74dacffd35c7bb09b3a1328"
+checksum = "134c189feb4956b20f6f547d2cf727d4c0fe06722b20a0eec87ed445a97f92da"
 dependencies = [
  "unicode-ident",
 ]
@@ -1432,9 +1430,9 @@ dependencies = [
 
 [[package]]
 name = "regex"
-version = "1.9.6"
+version = "1.10.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ebee201405406dbf528b8b672104ae6d6d63e6d118cb10e4d51abbc7b58044ff"
+checksum = "380b951a9c5e80ddfd6136919eef32310721aa4aacd4889a8d39124b026ab343"
 dependencies = [
  "aho-corasick",
  "memchr",
@@ -1444,9 +1442,9 @@ dependencies = [
 
 [[package]]
 name = "regex-automata"
-version = "0.3.9"
+version = "0.4.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "59b23e92ee4318893fa3fe3e6fb365258efbfe6ac6ab30f090cdcbb7aa37efa9"
+checksum = "5f804c7828047e88b2d32e2d7fe5a105da8ee3264f01902f796c8e067dc2483f"
 dependencies = [
  "aho-corasick",
  "memchr",
@@ -1455,9 +1453,9 @@ dependencies = [
 
 [[package]]
 name = "regex-syntax"
-version = "0.7.5"
+version = "0.8.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da"
+checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f"
 
 [[package]]
 name = "rustc_version"
@@ -1470,11 +1468,11 @@ dependencies = [
 
 [[package]]
 name = "rustix"
-version = "0.38.17"
+version = "0.38.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f25469e9ae0f3d0047ca8b93fc56843f38e6774f0914a107ff8b41be8be8e0b7"
+checksum = "745ecfa778e66b2b63c88a61cb36e0eea109e803b0b86bf9879fbc77c70e86ed"
 dependencies = [
- "bitflags 2.4.0",
+ "bitflags 2.4.1",
  "errno",
  "libc",
  "linux-raw-sys",
@@ -1525,22 +1523,22 @@ checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
 [[package]]
 name = "serde"
-version = "1.0.188"
+version = "1.0.189"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cf9e0fcba69a370eed61bcf2b728575f726b50b55cba78064753d708ddc7549e"
+checksum = "8e422a44e74ad4001bdc8eede9a4570ab52f71190e9c076d14369f38b9200537"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.188"
+version = "1.0.189"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4eca7ac642d82aa35b60049a6eccb4be6be75e599bd2e9adb5f875a737654af2"
+checksum = "1e48d1f918009ce3145511378cf68d613e3b3d9137d67272562080d68a2b32d5"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.37",
+ "syn 2.0.38",
 ]
 
 [[package]]
@@ -1633,15 +1631,15 @@ checksum = "290d54ea6f91c969195bdbcd7442c8c2a2ba87da8bf60a7ee86a235d4bc1e125"
 
 [[package]]
 name = "strum_macros"
-version = "0.25.2"
+version = "0.25.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ad8d03b598d3d0fff69bf533ee3ef19b8eeb342729596df84bcc7e1f96ec4059"
+checksum = "23dc1fa9ac9c169a78ba62f0b841814b7abae11bdd047b9c58f893439e309ea0"
 dependencies = [
  "heck",
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.37",
+ "syn 2.0.38",
 ]
 
 [[package]]
@@ -1657,9 +1655,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.37"
+version = "2.0.38"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7303ef2c05cd654186cb250d29049a24840ca25d2747c25c0381c8d9e2f582e8"
+checksum = "e96b79aaa137db8f61e26363a0c9b47d8b4ec75da28b7d1d614c2303e232408b"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1696,19 +1694,20 @@ checksum = "10712f02019e9288794769fba95cd6847df9874d49d871d062172f9dd41bc4cc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.37",
+ "syn 2.0.38",
 ]
 
 [[package]]
 name = "time"
-version = "0.3.29"
+version = "0.3.30"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "426f806f4089c493dcac0d24c29c01e2c38baf8e30f1b716ee37e83d200b18fe"
+checksum = "c4a34ab300f2dee6e562c10a046fc05e358b29f9bf92277f30c3c8d82275f6f5"
 dependencies = [
  "deranged",
  "itoa",
  "libc",
  "num_threads",
+ "powerfmt",
  "serde",
  "time-core",
  "time-macros",
@@ -1862,7 +1861,7 @@ dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.37",
+ "syn 2.0.38",
  "wasm-bindgen-shared",
 ]
 
@@ -1884,7 +1883,7 @@ checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.37",
+ "syn 2.0.38",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
@@ -1907,9 +1906,9 @@ dependencies = [
 
 [[package]]
 name = "wide"
-version = "0.7.12"
+version = "0.7.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ebecebefc38ff1860b4bc47550bbfa63af5746061cf0d29fcd7fa63171602598"
+checksum = "c68938b57b33da363195412cfc5fc37c9ed49aa9cfe2156fde64b8d2c9498242"
 dependencies = [
  "bytemuck",
  "safe_arch",
diff --git a/Cargo.toml b/Cargo.toml
index 95bf462..28a1acf 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -26,7 +26,7 @@ min-max-heap = { git = "https://github.com/tov/min-max-heap-rs", branch = "maste
 slab = "0.4"
 anyhow = "1.0"
 mimalloc = { version = "0.1", default-features = false }
-noodles = { version = "0.52", features = ["bam", "bgzf", "core", "cram", "fasta", "fastq", "sam"] }
+noodles = { version = "0.53", features = ["bam", "bgzf", "core", "cram", "fasta", "fastq", "sam"] }
 time = { version = "0.3", features = ["local-offset"] }
 flate2 = "1.0"