From 71ecd3f0166aa98b007838fc881cd703166fb676 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Nov 2024 23:15:56 +0000
Subject: [PATCH] Bump rust-htslib from 0.46.0 to 0.48.0

Bumps [rust-htslib](https://github.com/rust-bio/rust-htslib) from 0.46.0 to 0.48.0.
- [Release notes](https://github.com/rust-bio/rust-htslib/releases)
- [Changelog](https://github.com/rust-bio/rust-htslib/blob/master/CHANGELOG.md)
- [Commits](https://github.com/rust-bio/rust-htslib/compare/v0.46.0...v0.48.0)

---
updated-dependencies:
- dependency-name: rust-htslib
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Cargo.lock | 151 ++++++++++++++++++++++++++++++++++++++++++++---------
 Cargo.toml |   2 +-
 2 files changed, 126 insertions(+), 27 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index bdfd5da..c22308d 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -96,7 +96,7 @@ dependencies = [
  "rand_xoshiro",
  "rayon",
  "serde",
- "thiserror",
+ "thiserror 1.0.65",
 ]
 
 [[package]]
@@ -111,7 +111,7 @@ dependencies = [
  "num-integer",
  "num-traits",
  "rand",
- "thiserror",
+ "thiserror 1.0.65",
 ]
 
 [[package]]
@@ -154,6 +154,26 @@ dependencies = [
  "serde",
 ]
 
+[[package]]
+name = "bindgen"
+version = "0.69.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "271383c67ccabffb7381723dea0672a673f292304fcb45c01cc648c7a8d58088"
+dependencies = [
+ "bitflags",
+ "cexpr",
+ "clang-sys",
+ "itertools 0.11.0",
+ "lazy_static",
+ "lazycell",
+ "proc-macro2",
+ "quote",
+ "regex",
+ "rustc-hash",
+ "shlex",
+ "syn 2.0.87",
+]
+
 [[package]]
 name = "bio"
 version = "1.6.0"
@@ -188,7 +208,7 @@ dependencies = [
  "statrs 0.16.1",
  "strum",
  "strum_macros 0.25.3",
- "thiserror",
+ "thiserror 1.0.65",
  "triple_accel",
  "vec_map",
 ]
@@ -203,7 +223,7 @@ dependencies = [
  "lazy_static",
  "regex",
  "strum_macros 0.26.4",
- "thiserror",
+ "thiserror 1.0.65",
 ]
 
 [[package]]
@@ -277,12 +297,32 @@ dependencies = [
  "shlex",
 ]
 
+[[package]]
+name = "cexpr"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6fac387a98bb7c37292057cffc56d62ecb629900026402633ae9160df93a8766"
+dependencies = [
+ "nom",
+]
+
 [[package]]
 name = "cfg-if"
 version = "1.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
+[[package]]
+name = "clang-sys"
+version = "1.8.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b023947811758c97c59bf9d1c188fd619ad4718dcaa767947df1cadb14f39f4"
+dependencies = [
+ "glob",
+ "libc",
+ "libloading",
+]
+
 [[package]]
 name = "clap"
 version = "4.5.20"
@@ -314,7 +354,7 @@ dependencies = [
  "heck 0.5.0",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -425,24 +465,24 @@ dependencies = [
 
 [[package]]
 name = "derive-new"
-version = "0.5.9"
+version = "0.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535"
+checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 1.0.109",
+ "syn 2.0.87",
 ]
 
 [[package]]
 name = "derive-new"
-version = "0.6.0"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
+checksum = "2cdc8d50f426189eef89dac62fabfa0abb27d5cc008f25bf4156a0203325becc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -495,7 +535,7 @@ checksum = "f282cfdfe92516eb26c2af8589c274c7c17681f5ecc03c18255fe741c6aa64eb"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -602,6 +642,7 @@ version = "2.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e9f348d14cb4e50444e39fcd6b00302fe2ed2bc88094142f6278391d349a386d"
 dependencies = [
+ "bindgen",
  "bzip2-sys",
  "cc",
  "curl-sys",
@@ -722,12 +763,28 @@ version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
+[[package]]
+name = "lazycell"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55"
+
 [[package]]
 name = "libc"
 version = "0.2.161"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8e9489c2807c139ffd9c1794f4af0ebe86a828db53ecdc7fea2111d0fed085d1"
 
+[[package]]
+name = "libloading"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4979f22fdb869068da03c9f7528f8297c6fd2606bc3a4affe42e6a823fdb8da4"
+dependencies = [
+ "cfg-if",
+ "windows-targets",
+]
+
 [[package]]
 name = "libm"
 version = "0.2.8"
@@ -796,6 +853,12 @@ version = "2.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
+[[package]]
+name = "minimal-lexical"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
+
 [[package]]
 name = "multimap"
 version = "0.9.1"
@@ -860,7 +923,7 @@ checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -921,6 +984,16 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "nom"
+version = "7.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a"
+dependencies = [
+ "memchr",
+ "minimal-lexical",
+]
+
 [[package]]
 name = "num-complex"
 version = "0.4.6"
@@ -1153,7 +1226,7 @@ checksum = "ba009ff324d1fc1b900bd1fdb31564febe58a8ccc8a6fdbb93b543d33b13ca43"
 dependencies = [
  "getrandom",
  "libredox",
- "thiserror",
+ "thiserror 1.0.65",
 ]
 
 [[package]]
@@ -1187,14 +1260,14 @@ checksum = "2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c"
 
 [[package]]
 name = "rust-htslib"
-version = "0.46.0"
+version = "0.48.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "aec6f9ca4601beb4ae75ff8c99144dd15de5a873f6adf058da299962c760968e"
+checksum = "8313d0733b0a2782231fd7259e8f0873cb2542657719e06179811f86f8f797af"
 dependencies = [
  "bio-types",
  "byteorder",
  "custom_derive",
- "derive-new 0.5.9",
+ "derive-new 0.7.0",
  "hts-sys",
  "ieee754",
  "lazy_static",
@@ -1203,10 +1276,16 @@ dependencies = [
  "linear-map",
  "newtype_derive",
  "regex",
- "thiserror",
+ "thiserror 2.0.3",
  "url",
 ]
 
+[[package]]
+name = "rustc-hash"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2"
+
 [[package]]
 name = "rustc_version"
 version = "0.1.7"
@@ -1292,7 +1371,7 @@ checksum = "7e85ad2009c50b58e87caa8cd6dac16bdf511bbfb7af6c33df902396aa480fa5"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1439,7 +1518,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1452,7 +1531,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1468,9 +1547,9 @@ 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",
@@ -1500,7 +1579,16 @@ version = "1.0.65"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5d11abd9594d9b38965ef50805c5e469ca9cc6f197f883f717e0269a3057b3d5"
 dependencies = [
- "thiserror-impl",
+ "thiserror-impl 1.0.65",
+]
+
+[[package]]
+name = "thiserror"
+version = "2.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c006c85c7651b3cf2ada4584faa36773bd07bac24acfb39f3c431b36d7e667aa"
+dependencies = [
+ "thiserror-impl 2.0.3",
 ]
 
 [[package]]
@@ -1511,7 +1599,18 @@ checksum = "ae71770322cbd277e69d762a16c444af02aa0575ac0d174f0b9562d3b37f8602"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
+]
+
+[[package]]
+name = "thiserror-impl"
+version = "2.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f077553d607adc1caf65430528a576c757a71ed73944b66ebb58ef2bbd243568"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.87",
 ]
 
 [[package]]
@@ -1773,5 +1872,5 @@ checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn 2.0.87",
 ]
diff --git a/Cargo.toml b/Cargo.toml
index 028978c..99be38b 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -28,7 +28,7 @@ ndarray-ndimage = "0.4.0"
 rand = { version = "0.8.5", features = ["small_rng"] }
 rand_xoshiro = "0.6.0"
 rayon = "1.8.1"
-rust-htslib = "0.46.0"
+rust-htslib = "0.48.0"
 serde = "1.0.197"
 serde_json = "1.0.114"
 slog = "2.7.0"