From 8fa3296e54e71f1de67379e305dfe6cb23d6a5dc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 21:23:34 +0000
Subject: [PATCH] Bump rust-htslib from 0.46.0 to 0.47.0

Bumps [rust-htslib](https://github.com/rust-bio/rust-htslib) from 0.46.0 to 0.47.0.
- [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...v0.47.0)

---
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 | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++--
 Cargo.toml |  2 +-
 2 files changed, 82 insertions(+), 3 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index bdfd5da..7afd893 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -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 2.0.85",
+]
+
 [[package]]
 name = "bio"
 version = "1.6.0"
@@ -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"
@@ -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"
@@ -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"
@@ -1187,9 +1260,9 @@ checksum = "2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c"
 
 [[package]]
 name = "rust-htslib"
-version = "0.46.0"
+version = "0.47.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "aec6f9ca4601beb4ae75ff8c99144dd15de5a873f6adf058da299962c760968e"
+checksum = "41f1796800e73ebb282c6fc5c03f1fe160e867e01114a58a7e115ee3c1d02482"
 dependencies = [
  "bio-types",
  "byteorder",
@@ -1207,6 +1280,12 @@ dependencies = [
  "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"
diff --git a/Cargo.toml b/Cargo.toml
index 028978c..484af0b 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 = "0.47.0"
 serde = "1.0.197"
 serde_json = "1.0.114"
 slog = "2.7.0"