bam_compo

Cargo.lock

@@ -11,11 +11,60 @@ dependencies = [
  "memchr",
 ]
 
+[[package]]
+name = "anstream"
+version = "0.6.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b"
+dependencies = [
+ "anstyle",
+ "anstyle-parse",
+ "anstyle-query",
+ "anstyle-wincon",
+ "colorchoice",
+ "is_terminal_polyfill",
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle"
+version = "1.0.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b"
+
+[[package]]
+name = "anstyle-parse"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4"
+dependencies = [
+ "utf8parse",
+]
+
+[[package]]
+name = "anstyle-query"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391"
+dependencies = [
+ "windows-sys",
+]
+
+[[package]]
+name = "anstyle-wincon"
+version = "3.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19"
+dependencies = [
+ "anstyle",
+ "windows-sys",
+]
+
 [[package]]
 name = "anyhow"
-version = "1.0.83"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "25bdb32cbbdce2b519a9cd7df3a678443100e265d5e25ca763b7572a5104f5f3"
+checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da"
 
 [[package]]
 name = "autocfg"
@@ -25,15 +74,35 @@ checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
 
 [[package]]
 name = "average"
-version = "0.14.2"
+version = "0.15.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c309b1c7fca12ebeec3ecba29ea917b3a4cb458ccf504df68bb4d8a0ca565a00"
+checksum = "3a237a6822e1c3c98e700b6db5b293eb341b7524dcb8d227941245702b7431dc"
 dependencies = [
  "easy-cast",
  "float-ord",
  "num-traits",
 ]
 
+[[package]]
+name = "bindgen"
+version = "0.69.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a00dc851838a2120612785d195287475a3ac45514741da670b735818822129a0"
+dependencies = [
+ "bitflags",
+ "cexpr",
+ "clang-sys",
+ "itertools",
+ "lazy_static",
+ "lazycell",
+ "proc-macro2",
+ "quote",
+ "regex",
+ "rustc-hash",
+ "shlex",
+ "syn 2.0.64",
+]
+
 [[package]]
 name = "bio-types"
 version = "1.0.1"
@@ -47,6 +116,12 @@ dependencies = [
  "thiserror",
 ]
 
+[[package]]
+name = "bitflags"
+version = "2.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
+
 [[package]]
 name = "byteorder"
 version = "1.5.0"
@@ -75,6 +150,32 @@ dependencies = [
  "once_cell",
 ]
 
+[[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 = "cmake"
 version = "0.1.50"
@@ -84,6 +185,12 @@ dependencies = [
  "cc",
 ]
 
+[[package]]
+name = "colorchoice"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422"
+
 [[package]]
 name = "crossbeam-deque"
 version = "0.8.5"
@@ -156,17 +263,27 @@ version = "1.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3dca9240753cf90908d7e4aac30f630662b02aebaa1b58a3cadabdb23385b58b"
 
+[[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 = "0.11.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580"
+checksum = "38b35839ba51819680ba087cd351788c9a3c476841207e0b8cee0b04722343b9"
 dependencies = [
+ "anstream",
+ "anstyle",
+ "env_filter",
  "humantime",
- "is-terminal",
  "log",
- "regex",
- "termcolor",
 ]
 
 [[package]]
@@ -205,18 +322,13 @@ version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
-[[package]]
-name = "hermit-abi"
-version = "0.3.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024"
-
 [[package]]
 name = "hts-sys"
 version = "2.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e9f348d14cb4e50444e39fcd6b00302fe2ed2bc88094142f6278391d349a386d"
 dependencies = [
+ "bindgen",
  "bzip2-sys",
  "cc",
  "curl-sys",
@@ -250,14 +362,18 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c"
 
 [[package]]
-name = "is-terminal"
-version = "0.4.12"
+name = "is_terminal_polyfill"
+version = "1.70.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b"
+checksum = "f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800"
+
+[[package]]
+name = "itertools"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569"
 dependencies = [
- "hermit-abi",
- "libc",
- "windows-sys",
+ "either",
 ]
 
 [[package]]
@@ -275,12 +391,28 @@ version = "1.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
 
+[[package]]
+name = "lazycell"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55"
+
 [[package]]
 name = "libc"
 version = "0.2.153"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
 
+[[package]]
+name = "libloading"
+version = "0.8.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e310b3a6b5907f99202fcdb4960ff45b93735d7c7d96b760fcff8db2dc0e103d"
+dependencies = [
+ "cfg-if",
+ "windows-targets",
+]
+
 [[package]]
 name = "libm"
 version = "0.2.8"
@@ -308,9 +440,9 @@ checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
 
 [[package]]
 name = "log"
-version = "0.4.21"
+version = "0.4.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
+checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
 
 [[package]]
 name = "lzma-sys"
@@ -329,6 +461,12 @@ version = "2.7.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
 
+[[package]]
+name = "minimal-lexical"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
+
 [[package]]
 name = "newtype_derive"
 version = "0.1.6"
@@ -338,6 +476,16 @@ dependencies = [
  "rustc_version",
 ]
 
+[[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-traits"
 version = "0.2.19"
@@ -475,9 +623,9 @@ checksum = "adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56"
 
 [[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",
@@ -495,6 +643,12 @@ 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"
@@ -516,6 +670,12 @@ version = "0.1.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
+[[package]]
+name = "shlex"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
+
 [[package]]
 name = "strum_macros"
 version = "0.25.3"
@@ -551,15 +711,6 @@ dependencies = [
  "unicode-ident",
 ]
 
-[[package]]
-name = "termcolor"
-version = "1.4.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755"
-dependencies = [
- "winapi-util",
-]
-
 [[package]]
 name = "thiserror"
 version = "1.0.60"
@@ -628,19 +779,16 @@ dependencies = [
 ]
 
 [[package]]
-name = "vcpkg"
-version = "0.2.15"
+name = "utf8parse"
+version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
+checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
 
 [[package]]
-name = "winapi-util"
-version = "0.1.8"
+name = "vcpkg"
+version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
-dependencies = [
- "windows-sys",
-]
+checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
 
 [[package]]
 name = "windows-sys"

Cargo.toml

@@ -6,11 +6,11 @@ edition = "2021"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-rust-htslib = "0.46.0"
-anyhow = "^1.0.75"
-average = "0.14.1"
-rayon = "1.9.0"
-log = "^0.4.20"
-env_logger = "^0.10.1"
+rust-htslib = "0.47.0"
+anyhow = "^1.0.86"
+average = "0.15.1"
+rayon = "1.10.0"
+log = "^0.4.22"
+env_logger = "^0.11.3"