From cade02a2555c1363e72f73e069c96ce5db634b2d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 7 Aug 2023 22:47:49 +0000
Subject: [PATCH] Bump rust-htslib from 0.20.0 to 0.44.1

Bumps [rust-htslib](https://github.com/rust-bio/rust-htslib) from 0.20.0 to 0.44.1.
- [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/0.20.0...v0.44.1)

---
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 | 483 +++++++++++++++++++++++++++--------------------------
 Cargo.toml |   2 +-
 2 files changed, 244 insertions(+), 241 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index a811222..ff6becc 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -17,22 +17,13 @@ version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "567b077b825e468cc974f0020d4082ee6e03132512f207ef1a02fd5d00d1f32d"
 
-[[package]]
-name = "aho-corasick"
-version = "0.6.10"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "81ce3d38065e618af2d7b77e10c5ad9a069859b4be3c2250f674af3840d9c8a5"
-dependencies = [
- "memchr 2.3.3",
-]
-
 [[package]]
 name = "aho-corasick"
 version = "0.7.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8716408b8bc624ed7f65d223ddb9ac2d044c0547b6fa4b0d554f3a9540496ada"
 dependencies = [
- "memchr 2.3.3",
+ "memchr",
 ]
 
 [[package]]
@@ -94,31 +85,18 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b41b7ea54a0c9d92199de89e20e58d49f02f8e699814ef3fdf266f6f748d15c7"
 
 [[package]]
-name = "bindgen"
-version = "0.36.1"
+name = "bio-types"
+version = "1.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "acc8fa644dc2b6f6c2d391ccea460da1ad9bf2271c4e9ffaad88d2dd727a7295"
+checksum = "c915bf6c578d40e1e497f8c571a4514bc89c3195cec2abb8be6dd5500405c752"
 dependencies = [
- "cexpr",
- "cfg-if",
- "clang-sys",
- "clap",
- "env_logger",
- "lazy_static 1.4.0",
- "log",
- "peeking_take_while",
- "proc-macro2 0.3.5",
- "quote 0.5.2",
- "regex 0.2.11",
- "which",
+ "derive-new",
+ "lazy_static",
+ "regex",
+ "strum_macros",
+ "thiserror",
 ]
 
-[[package]]
-name = "bitflags"
-version = "0.9.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4efd02e230a02e18f92fc2735f44597385ed02ad8f831e7c1c1156ee5e1ab3a5"
-
 [[package]]
 name = "bitflags"
 version = "1.2.1"
@@ -142,8 +120,8 @@ version = "0.2.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "31accafdb70df7871592c058eca3985b71104e15ac32f64706022c58867da931"
 dependencies = [
- "lazy_static 1.4.0",
- "memchr 2.3.3",
+ "lazy_static",
+ "memchr",
  "regex-automata",
  "serde",
 ]
@@ -155,18 +133,24 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "08c48aae112d48ed9f069b33538ea9e3e90aa263cfa3d1c24309612b1f7472de"
 
 [[package]]
-name = "cc"
-version = "1.0.54"
+name = "bzip2-sys"
+version = "0.1.11+1.0.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7bbb73db36c1246e9034e307d0fba23f9a2e251faa47ade70c1bd252220c8311"
+checksum = "736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc"
+dependencies = [
+ "cc",
+ "libc",
+ "pkg-config",
+]
 
 [[package]]
-name = "cexpr"
-version = "0.2.3"
+name = "cc"
+version = "1.0.82"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "42aac45e9567d97474a834efdee3081b3c942b2205be932092f53354ce503d6c"
+checksum = "305fe645edc1442a0fa8b6726ba61d422798d37a52e12eaecf4b022ebbb88f01"
 dependencies = [
- "nom",
+ "jobserver",
+ "libc",
 ]
 
 [[package]]
@@ -186,17 +170,6 @@ dependencies = [
  "time",
 ]
 
-[[package]]
-name = "clang-sys"
-version = "0.22.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "939a1a34310b120d26eba35c29475933128b0ec58e24b43327f8dbe6036fc538"
-dependencies = [
- "glob",
- "libc",
- "libloading",
-]
-
 [[package]]
 name = "clap"
 version = "2.33.1"
@@ -205,13 +178,22 @@ checksum = "bdfa80d47f954d53a35a64987ca1422f495b8d6483c0fe9f7117b36c2a792129"
 dependencies = [
  "ansi_term",
  "atty",
- "bitflags 1.2.1",
+ "bitflags",
  "strsim",
  "textwrap",
  "unicode-width",
  "vec_map",
 ]
 
+[[package]]
+name = "cmake"
+version = "0.1.50"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130"
+dependencies = [
+ "cc",
+]
+
 [[package]]
 name = "constant_time_eq"
 version = "0.1.5"
@@ -238,7 +220,7 @@ dependencies = [
  "autocfg",
  "cfg-if",
  "crossbeam-utils",
- "lazy_static 1.4.0",
+ "lazy_static",
  "maybe-uninit",
  "memoffset",
  "scopeguard",
@@ -263,7 +245,7 @@ checksum = "c3c7c73a2d1e9fc0886a08b93e98eb643461230d5f1925e4036204d5f2e261a8"
 dependencies = [
  "autocfg",
  "cfg-if",
- "lazy_static 1.4.0",
+ "lazy_static",
 ]
 
 [[package]]
@@ -285,7 +267,22 @@ version = "0.1.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90"
 dependencies = [
- "memchr 2.3.3",
+ "memchr",
+]
+
+[[package]]
+name = "curl-sys"
+version = "0.4.65+curl-8.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "961ba061c9ef2fe34bbd12b807152d96f0badd2bebe7b90ce6c8c8b7572a0986"
+dependencies = [
+ "cc",
+ "libc",
+ "libz-sys",
+ "openssl-sys",
+ "pkg-config",
+ "vcpkg",
+ "winapi",
 ]
 
 [[package]]
@@ -300,6 +297,17 @@ version = "2.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "72aa14c04dfae8dd7d8a2b1cb7ca2152618cd01336dbfe704b8dcbf8d41dbd69"
 
+[[package]]
+name = "derive-new"
+version = "0.5.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "dirs"
 version = "1.0.5"
@@ -317,26 +325,13 @@ version = "1.5.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bb1f6b1ce1c140482ea30ddd3335fc0024ac7ee112895426e0a629a6c20adfe3"
 
-[[package]]
-name = "env_logger"
-version = "0.5.13"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "15b0a4d2e39f8420210be8b27eeda28029729e2fd4291019455016c348240c38"
-dependencies = [
- "atty",
- "humantime",
- "log",
- "regex 1.3.9",
- "termcolor",
-]
-
 [[package]]
 name = "faccess"
 version = "0.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e039175679baf763ddddf4f76900b92d4dae9411ee88cf42d2f11b976b09e07c"
 dependencies = [
- "bitflags 1.2.1",
+ "bitflags",
  "libc",
  "winapi",
 ]
@@ -357,12 +352,21 @@ version = "0.1.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "aa4da3c766cd7a0db8242e326e9e4e081edd567072893ed320008189715366a4"
 dependencies = [
- "proc-macro2 1.0.18",
- "quote 1.0.7",
+ "proc-macro2",
+ "quote",
  "syn",
  "synstructure",
 ]
 
+[[package]]
+name = "form_urlencoded"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652"
+dependencies = [
+ "percent-encoding",
+]
+
 [[package]]
 name = "fs-utils"
 version = "1.1.4"
@@ -391,9 +395,15 @@ checksum = "bcc8e0c9bce37868955864dbecd2b1ab2bdf967e6f28066d65aaac620444b65c"
 
 [[package]]
 name = "glob"
-version = "0.2.11"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
+
+[[package]]
+name = "heck"
+version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8be18de09a56b60ed0edf84bc9df007e30040691af7acd1c41874faac5895bfb"
+checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
 [[package]]
 name = "hermit-abi"
@@ -404,6 +414,22 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "hts-sys"
+version = "2.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "deebfb779c734d542e7f14c298597914b9b5425e4089aef482eacb5cab941915"
+dependencies = [
+ "bzip2-sys",
+ "cc",
+ "curl-sys",
+ "fs-utils",
+ "glob",
+ "libz-sys",
+ "lzma-sys",
+ "openssl-sys",
+]
+
 [[package]]
 name = "human-panic"
 version = "1.0.3"
@@ -419,22 +445,12 @@ dependencies = [
  "uuid",
 ]
 
-[[package]]
-name = "humantime"
-version = "1.3.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "df004cfca50ef23c36850aaaa59ad52cc70d0e90243c3c7737a4dd32dc7a3c4f"
-dependencies = [
- "quick-error",
-]
-
 [[package]]
 name = "idna"
-version = "0.1.5"
+version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "38f09e0f0b1fb55fdee1f17470ad800da77af5186a1a76c026b679358b7e844e"
+checksum = "7d20d6b07bfbc108882d88ed8e37d39636dcc260e15e30c45e6ba089610b917c"
 dependencies = [
- "matches",
  "unicode-bidi",
  "unicode-normalization",
 ]
@@ -445,15 +461,6 @@ version = "0.2.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c"
 
-[[package]]
-name = "itertools"
-version = "0.6.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d3f2be4da1690a039e9ae5fd575f706a63ad5a2120f161b1d653c9da3930dd21"
-dependencies = [
- "either",
-]
-
 [[package]]
 name = "itoa"
 version = "0.4.6"
@@ -461,10 +468,13 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dc6f3ad7b9d11a0c00842ff8de1b60ee58661048eb8049ed33c73594f359d7e6"
 
 [[package]]
-name = "lazy_static"
-version = "0.2.11"
+name = "jobserver"
+version = "0.1.26"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "76f033c7ad61445c5b347c7382dd1237847eb1bce590fe50365dcb33d546be73"
+checksum = "936cfd212a0155903bcbc060e316fb6cc7cbf2e1907329391ebadc1fe0ce77c2"
+dependencies = [
+ "libc",
+]
 
 [[package]]
 name = "lazy_static"
@@ -479,13 +489,16 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9457b06509d27052635f90d6466700c65095fdf75409b3fbdd903e988b886f49"
 
 [[package]]
-name = "libloading"
-version = "0.5.2"
+name = "libz-sys"
+version = "1.1.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f2b111a074963af1d37a139918ac6d49ad1d0d5e47f72fd55388619691a7d753"
+checksum = "d97137b25e321a73eef1418d1d5d2eda4d77e12813f8e6dead84bc52c5870a7b"
 dependencies = [
  "cc",
- "winapi",
+ "cmake",
+ "libc",
+ "pkg-config",
+ "vcpkg",
 ]
 
 [[package]]
@@ -501,10 +514,15 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b06a4cde4c0f271a446782e3eff8de789548ce57dbc8eca9292c27f4a42004b4"
 
 [[package]]
-name = "matches"
-version = "0.1.8"
+name = "lzma-sys"
+version = "0.1.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ffc5c5338469d4d3ea17d269fa8ea3512ad247247c30bd2df69e68309ed0a08"
+checksum = "5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27"
+dependencies = [
+ "cc",
+ "libc",
+ "pkg-config",
+]
 
 [[package]]
 name = "maybe-uninit"
@@ -512,15 +530,6 @@ version = "2.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "60302e4db3a61da70c0cb7991976248362f30319e88850c487b9b95bbf059e00"
 
-[[package]]
-name = "memchr"
-version = "1.0.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "148fab2e51b4f1cfc66da2a7c32981d1d3c083a803978268bb11fe4b86925e7a"
-dependencies = [
- "libc",
-]
-
 [[package]]
 name = "memchr"
 version = "2.3.3"
@@ -554,15 +563,6 @@ dependencies = [
  "rustc_version",
 ]
 
-[[package]]
-name = "nom"
-version = "3.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "05aec50c70fd288702bcd93284a8444607f3292dbdf2a30de5ea5dcdbe72287b"
-dependencies = [
- "memchr 1.0.2",
-]
-
 [[package]]
 name = "num-integer"
 version = "0.1.43"
@@ -598,26 +598,48 @@ version = "0.20.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1ab52be62400ca80aa00285d25253d7f7c437b7375c4de678f5405d3afe82ca5"
 
+[[package]]
+name = "openssl-src"
+version = "111.27.0+1.1.1v"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "06e8f197c82d7511c5b014030c9b1efeda40d7d5f99d23b4ceed3524a5e63f02"
+dependencies = [
+ "cc",
+]
+
+[[package]]
+name = "openssl-sys"
+version = "0.9.91"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "866b5f16f90776b9bb8dc1e1802ac6f0513de3a7a7465867bfbc563dc737faac"
+dependencies = [
+ "cc",
+ "libc",
+ "openssl-src",
+ "pkg-config",
+ "vcpkg",
+]
+
 [[package]]
 name = "os_type"
 version = "2.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7edc011af0ae98b7f88cf7e4a83b70a54a75d2b8cb013d6efd02e5956207e9eb"
 dependencies = [
- "regex 1.3.9",
+ "regex",
 ]
 
 [[package]]
-name = "peeking_take_while"
-version = "0.1.2"
+name = "percent-encoding"
+version = "2.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "19b17cddbe7ec3f8bc800887bab5e717348c95ea2ca0b1bf0837fb964dc67099"
+checksum = "9b2a4787296e9989611394c33f193f676704af1686e70b8f8033ab5ba9a35a94"
 
 [[package]]
-name = "percent-encoding"
-version = "1.0.1"
+name = "pkg-config"
+version = "0.3.27"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "31010dd2e1ac33d5b46a5b413495239882813e0369f8ed8a5e266f173602f831"
+checksum = "26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964"
 
 [[package]]
 name = "ppv-lite86"
@@ -627,20 +649,11 @@ checksum = "237a5ed80e274dbc66f86bd59c1e25edc039660be53194b5fe0a482e0f2612ea"
 
 [[package]]
 name = "proc-macro2"
-version = "0.3.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77997c53ae6edd6d187fec07ec41b207063b5ee6f33680e9fa86d405cdd313d4"
-dependencies = [
- "unicode-xid 0.1.0",
-]
-
-[[package]]
-name = "proc-macro2"
-version = "1.0.18"
+version = "1.0.66"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "beae6331a816b1f65d04c45b078fd8e6c93e8071771f41b8163255bbd8d7c8fa"
+checksum = "18fb31db3f9bddb2ea821cde30a9f70117e3f119938b5ee630b7403aa6e2ead9"
 dependencies = [
- "unicode-xid 0.2.0",
+ "unicode-ident",
 ]
 
 [[package]]
@@ -649,22 +662,13 @@ version = "1.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
 
-[[package]]
-name = "quote"
-version = "0.5.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9949cfe66888ffe1d53e6ec9d9f3b70714083854be20fd5e271b232a017401e8"
-dependencies = [
- "proc-macro2 0.3.5",
-]
-
 [[package]]
 name = "quote"
 version = "1.0.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "aa563d17ecb180e500da1cfd2b028310ac758de548efdd203e18f283af693f37"
 dependencies = [
- "proc-macro2 1.0.18",
+ "proc-macro2",
 ]
 
 [[package]]
@@ -729,7 +733,7 @@ dependencies = [
  "crossbeam-deque",
  "crossbeam-queue",
  "crossbeam-utils",
- "lazy_static 1.4.0",
+ "lazy_static",
  "num_cpus",
 ]
 
@@ -750,29 +754,16 @@ dependencies = [
  "rust-argon2",
 ]
 
-[[package]]
-name = "regex"
-version = "0.2.11"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9329abc99e39129fcceabd24cf5d85b4671ef7c29c50e972bc5afe32438ec384"
-dependencies = [
- "aho-corasick 0.6.10",
- "memchr 2.3.3",
- "regex-syntax 0.5.6",
- "thread_local 0.3.6",
- "utf8-ranges",
-]
-
 [[package]]
 name = "regex"
 version = "1.3.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9c3780fcf44b193bc4d09f36d2a3c87b251da4a046c87795a0d35f4f927ad8e6"
 dependencies = [
- "aho-corasick 0.7.10",
- "memchr 2.3.3",
- "regex-syntax 0.6.18",
- "thread_local 1.0.1",
+ "aho-corasick",
+ "memchr",
+ "regex-syntax",
+ "thread_local",
 ]
 
 [[package]]
@@ -784,15 +775,6 @@ dependencies = [
  "byteorder",
 ]
 
-[[package]]
-name = "regex-syntax"
-version = "0.5.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7d707a4fa2637f2dca2ef9fd02225ec7661fe01a53623c1e6515b6916511f7a7"
-dependencies = [
- "ucd-util",
-]
-
 [[package]]
 name = "regex-syntax"
 version = "0.6.18"
@@ -815,7 +797,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "426bc186e3e95cac1e4a4be125a4aca7e84c2d616ffc02244eef36e2a60a093c"
 dependencies = [
  "cc",
- "lazy_static 1.4.0",
+ "lazy_static",
  "libc",
  "spin",
  "untrusted",
@@ -836,22 +818,22 @@ dependencies = [
 
 [[package]]
 name = "rust-htslib"
-version = "0.20.0"
+version = "0.44.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f702eebd89609dd27605999d981b67b3380861cc2d4318a2e827709c884006c4"
+checksum = "7c7eb0f29fce64a4e22578905efef3d72389058016023279a58b282eb5c0c467"
 dependencies = [
- "bindgen",
- "bitflags 0.9.1",
+ "bio-types",
+ "byteorder",
  "custom_derive",
- "fs-utils",
+ "derive-new",
+ "hts-sys",
  "ieee754",
- "itertools",
- "lazy_static 0.2.11",
+ "lazy_static",
  "libc",
  "linear-map",
  "newtype_derive",
- "quick-error",
- "regex 1.3.9",
+ "regex",
+ "thiserror",
  "url",
 ]
 
@@ -870,6 +852,12 @@ dependencies = [
  "semver",
 ]
 
+[[package]]
+name = "rustversion"
+version = "1.0.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4"
+
 [[package]]
 name = "ryu"
 version = "1.0.5"
@@ -900,8 +888,8 @@ version = "1.0.113"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "93c5eaa17d0954cb481cdcfffe9d84fcfa7a1a9f2349271e678677be4c26ae31"
 dependencies = [
- "proc-macro2 1.0.18",
- "quote 1.0.7",
+ "proc-macro2",
+ "quote",
  "syn",
 ]
 
@@ -928,6 +916,19 @@ version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8ea5119cdb4c55b55d432abb513a0429384878c15dde60cc77b1c99de1a95a6a"
 
+[[package]]
+name = "strum_macros"
+version = "0.24.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e385be0d24f186b4ce2f9982191e7101bb737312ad61c1f2f984f34bcf85d59"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "quote",
+ "rustversion",
+ "syn",
+]
+
 [[package]]
 name = "subset-bam"
 version = "1.1.0"
@@ -949,13 +950,13 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "1.0.31"
+version = "1.0.109"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b5304cfdf27365b7585c25d4af91b35016ed21ef88f17ced89c7093b43dba8b6"
+checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
 dependencies = [
- "proc-macro2 1.0.18",
- "quote 1.0.7",
- "unicode-xid 0.2.0",
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
 ]
 
 [[package]]
@@ -964,10 +965,10 @@ version = "0.12.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b834f2d66f734cb897113e34aaff2f1ab4719ca946f9a7358dba8f8064148701"
 dependencies = [
- "proc-macro2 1.0.18",
- "quote 1.0.7",
+ "proc-macro2",
+ "quote",
  "syn",
- "unicode-xid 0.2.0",
+ "unicode-xid",
 ]
 
 [[package]]
@@ -1024,12 +1025,23 @@ dependencies = [
 ]
 
 [[package]]
-name = "thread_local"
-version = "0.3.6"
+name = "thiserror"
+version = "1.0.39"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c6b53e329000edc2b34dbe8545fd20e55a333362d0a321909685a19bd28c3f1b"
+checksum = "a5ab016db510546d856297882807df8da66a16fb8c4101cb8b30054b0d5b2d9c"
 dependencies = [
- "lazy_static 1.4.0",
+ "thiserror-impl",
+]
+
+[[package]]
+name = "thiserror-impl"
+version = "1.0.39"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5420d42e90af0c38c3290abcca25b9b3bdf379fc9f55c528f53a269d9c9a267e"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
 ]
 
 [[package]]
@@ -1038,7 +1050,7 @@ version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d40c6d1b69745a6ec6fb1ca717914848da4b44ae29d9b3080cbee91d72a69b14"
 dependencies = [
- "lazy_static 1.4.0",
+ "lazy_static",
 ]
 
 [[package]]
@@ -1053,9 +1065,18 @@ dependencies = [
 
 [[package]]
 name = "tinyvec"
-version = "0.3.3"
+version = "1.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "53953d2d3a5ad81d9f844a32f14ebb121f50b650cd59d0ee2a07cf13c617efed"
+checksum = "87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50"
+dependencies = [
+ "tinyvec_macros",
+]
+
+[[package]]
+name = "tinyvec_macros"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
 
 [[package]]
 name = "toml"
@@ -1067,25 +1088,22 @@ dependencies = [
 ]
 
 [[package]]
-name = "ucd-util"
-version = "0.1.8"
+name = "unicode-bidi"
+version = "0.3.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c85f514e095d348c279b1e5cd76795082cf15bd59b93207832abe0b1d8fed236"
+checksum = "92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460"
 
 [[package]]
-name = "unicode-bidi"
-version = "0.3.4"
+name = "unicode-ident"
+version = "1.0.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "49f2bd0c6468a8230e1db229cff8029217cf623c767ea5d60bfbd42729ea54d5"
-dependencies = [
- "matches",
-]
+checksum = "301abaae475aa91687eb82514b328ab47a211a533026cb25fc3e519b86adfc3c"
 
 [[package]]
 name = "unicode-normalization"
-version = "0.1.13"
+version = "0.1.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6fb19cf769fa8c6a80a162df694621ebeb4dafb606470b2b2fce0be40a98a977"
+checksum = "5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921"
 dependencies = [
  "tinyvec",
 ]
@@ -1096,12 +1114,6 @@ version = "0.1.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "caaa9d531767d1ff2150b9332433f32a24622147e5ebb1f26409d5da67afd479"
 
-[[package]]
-name = "unicode-xid"
-version = "0.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc"
-
 [[package]]
 name = "unicode-xid"
 version = "0.2.0"
@@ -1116,21 +1128,15 @@ checksum = "55cd1f4b4e96b46aeb8d4855db4a7a9bd96eeeb5c6a1ab54593328761642ce2f"
 
 [[package]]
 name = "url"
-version = "1.7.2"
+version = "2.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dd4e7c0d531266369519a4aa4f399d748bd37043b00bde1e4ff1f60a120b355a"
+checksum = "50bff7831e19200a85b17131d085c25d7811bc4e186efdaf54bbd132994a88cb"
 dependencies = [
+ "form_urlencoded",
  "idna",
- "matches",
  "percent-encoding",
 ]
 
-[[package]]
-name = "utf8-ranges"
-version = "1.0.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b4ae116fef2b7fea257ed6440d3cfcff7f190865f170cdad00bb6465bf18ecba"
-
 [[package]]
 name = "uuid"
 version = "0.8.1"
@@ -1140,6 +1146,12 @@ dependencies = [
  "rand",
 ]
 
+[[package]]
+name = "vcpkg"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
+
 [[package]]
 name = "vec_map"
 version = "0.8.2"
@@ -1152,15 +1164,6 @@ version = "0.9.0+wasi-snapshot-preview1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519"
 
-[[package]]
-name = "which"
-version = "1.0.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e84a603e7e0b1ce1aa1ee2b109c7be00155ce52df5081590d1ffb93f4f515cb2"
-dependencies = [
- "libc",
-]
-
 [[package]]
 name = "winapi"
 version = "0.3.8"
diff --git a/Cargo.toml b/Cargo.toml
index ca327aa..6f5fe10 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -4,7 +4,7 @@ version = "1.1.0"
 authors = ["Ian Fiddes <ian.fiddes@10xgenomics.com>", "Wyatt McDonnell <wyatt.mcdonnell@10xgenomics.com>"]
 
 [dependencies]
-rust-htslib = "0.20"
+rust-htslib = "0.44"
 csv = "1"
 failure = "*"
 clap = "*"