first

.gitignore

@@ -0,0 +1 @@
+/target

Cargo.lock

@@ -0,0 +1,1979 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 3
+
+[[package]]
+name = "adler"
+version = "1.0.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
+
+[[package]]
+name = "ahash"
+version = "0.8.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011"
+dependencies = [
+ "cfg-if",
+ "once_cell",
+ "version_check",
+ "zerocopy",
+]
+
+[[package]]
+name = "aho-corasick"
+version = "1.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916"
+dependencies = [
+ "memchr",
+]
+
+[[package]]
+name = "allocator-api2"
+version = "0.2.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5c6cb57a04249c6480766f7f7cef5467412af1490f8d1e243141daddada3264f"
+
+[[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 = "1.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a64c907d4e79225ac72e2a354c9ce84d50ebb4586dee56c82b3ee73004f537f5"
+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"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "25bdb32cbbdce2b519a9cd7df3a678443100e265d5e25ca763b7572a5104f5f3"
+
+[[package]]
+name = "approx"
+version = "0.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6"
+dependencies = [
+ "num-traits",
+]
+
+[[package]]
+name = "autocfg"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
+
+[[package]]
+name = "average"
+version = "0.14.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c309b1c7fca12ebeec3ecba29ea917b3a4cb458ccf504df68bb4d8a0ca565a00"
+dependencies = [
+ "easy-cast",
+ "float-ord",
+ "num-traits",
+]
+
+[[package]]
+name = "bgzip"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b64fd8980fb64af5951bc05de7772b598150a6f7eac42ec17f73e8489915f99b"
+dependencies = [
+ "flate2",
+ "log",
+ "rayon",
+ "thiserror",
+]
+
+[[package]]
+name = "bio-types"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9d45749b87f21808051025e9bf714d14ff4627f9d8ca967eade6946ea769aa4a"
+dependencies = [
+ "derive-new",
+ "lazy_static",
+ "regex",
+ "strum_macros",
+ "thiserror",
+]
+
+[[package]]
+name = "bit-vec"
+version = "0.6.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
+
+[[package]]
+name = "bitflags"
+version = "2.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cf4b9d6a944f767f8e5e0db018570623c85f3d925ac718db4e06d0187adb21c1"
+
+[[package]]
+name = "bytemuck"
+version = "1.16.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "78834c15cb5d5efe3452d58b1e8ba890dd62d21907f867f383358198e56ebca5"
+
+[[package]]
+name = "byteorder"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
+
+[[package]]
+name = "bytes"
+version = "1.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "514de17de45fdb8dc022b1a7975556c53c86f9f0aa5f534b98977b171857c2c9"
+
+[[package]]
+name = "bzip2-sys"
+version = "0.1.11+1.0.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc"
+dependencies = [
+ "cc",
+ "libc",
+ "pkg-config",
+]
+
+[[package]]
+name = "cc"
+version = "1.0.97"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "099a5357d84c4c61eb35fc8eafa9a79a902c2f76911e5747ced4e032edd8d9b4"
+dependencies = [
+ "jobserver",
+ "libc",
+ "once_cell",
+]
+
+[[package]]
+name = "cfg-if"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
+
+[[package]]
+name = "clap"
+version = "4.5.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "90bc066a67923782aa8515dbaea16946c5bcc5addbd668bb80af688e53e548a0"
+dependencies = [
+ "clap_builder",
+ "clap_derive",
+]
+
+[[package]]
+name = "clap_builder"
+version = "4.5.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4"
+dependencies = [
+ "anstream",
+ "anstyle",
+ "clap_lex",
+ "strsim",
+]
+
+[[package]]
+name = "clap_derive"
+version = "4.5.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "528131438037fd55894f62d6e9f068b8f45ac57ffa77517819645d10aed04f64"
+dependencies = [
+ "heck 0.5.0",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.64",
+]
+
+[[package]]
+name = "clap_lex"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce"
+
+[[package]]
+name = "cmake"
+version = "0.1.50"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130"
+dependencies = [
+ "cc",
+]
+
+[[package]]
+name = "colorchoice"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422"
+
+[[package]]
+name = "confy"
+version = "0.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e37668cb35145dcfaa1931a5f37fde375eeae8068b4c0d2f289da28a270b2d2c"
+dependencies = [
+ "directories",
+ "serde",
+ "thiserror",
+ "toml",
+]
+
+[[package]]
+name = "console"
+version = "0.15.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb"
+dependencies = [
+ "encode_unicode 0.3.6",
+ "lazy_static",
+ "libc",
+ "unicode-width",
+ "windows-sys",
+]
+
+[[package]]
+name = "crc32fast"
+version = "1.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b3855a8a784b474f333699ef2bbca9db2c4a1f6d9088a90a2d25b1eb53111eaa"
+dependencies = [
+ "cfg-if",
+]
+
+[[package]]
+name = "crossbeam"
+version = "0.8.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1137cd7e7fc0fb5d3c5a8678be38ec56e819125d8d7907411fe24ccb943faca8"
+dependencies = [
+ "crossbeam-channel",
+ "crossbeam-deque",
+ "crossbeam-epoch",
+ "crossbeam-queue",
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-channel"
+version = "0.5.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ab3db02a9c5b5121e1e42fbdb1aeb65f5e02624cc58c43f2884c6ccac0b82f95"
+dependencies = [
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-deque"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d"
+dependencies = [
+ "crossbeam-epoch",
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-epoch"
+version = "0.9.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e"
+dependencies = [
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-queue"
+version = "0.3.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "df0346b5d5e76ac2fe4e327c5fd1118d6be7c51dfb18f9b7922923f287471e35"
+dependencies = [
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-utils"
+version = "0.8.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345"
+
+[[package]]
+name = "crunchy"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7a81dae078cea95a014a339291cec439d2f232ebe854a9d672b796c6afafa9b7"
+
+[[package]]
+name = "csv"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ac574ff4d437a7b5ad237ef331c17ccca63c46479e5b5453eb8e10bb99a759fe"
+dependencies = [
+ "csv-core",
+ "itoa",
+ "ryu",
+ "serde",
+]
+
+[[package]]
+name = "csv-core"
+version = "0.1.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5efa2b3d7902f4b634a20cae3c9c4e6209dc4779feb6863329607560143efa70"
+dependencies = [
+ "memchr",
+]
+
+[[package]]
+name = "curl-sys"
+version = "0.4.72+curl-8.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29cbdc8314c447d11e8fd156dcdd031d9e02a7a976163e396b548c03153bc9ea"
+dependencies = [
+ "cc",
+ "libc",
+ "libz-sys",
+ "openssl-sys",
+ "pkg-config",
+ "vcpkg",
+ "windows-sys",
+]
+
+[[package]]
+name = "custom_derive"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
+
+[[package]]
+name = "dashmap"
+version = "5.5.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "978747c1d849a7d2ee5e8adc0159961c48fb7e5db2f06af6723b80123bb53856"
+dependencies = [
+ "cfg-if",
+ "hashbrown",
+ "lock_api",
+ "once_cell",
+ "parking_lot_core",
+ "rayon",
+ "serde",
+]
+
+[[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 1.0.109",
+]
+
+[[package]]
+name = "directories"
+version = "4.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f51c5d4ddabd36886dd3e1438cb358cdcb0d7c499cb99cb4ac2e38e18b5cb210"
+dependencies = [
+ "dirs-sys",
+]
+
+[[package]]
+name = "dirs-next"
+version = "2.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b98cf8ebf19c3d1b223e151f99a4f9f0690dca41414773390fc824184ac833e1"
+dependencies = [
+ "cfg-if",
+ "dirs-sys-next",
+]
+
+[[package]]
+name = "dirs-sys"
+version = "0.3.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1b1d1d91c932ef41c0f2663aa8b0ca0342d444d842c06914aa0a7e352d0bada6"
+dependencies = [
+ "libc",
+ "redox_users",
+ "winapi",
+]
+
+[[package]]
+name = "dirs-sys-next"
+version = "0.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4ebda144c4fe02d1f7ea1a7d9641b6fc6b580adcfa024ae48797ecdeb6825b4d"
+dependencies = [
+ "libc",
+ "redox_users",
+ "winapi",
+]
+
+[[package]]
+name = "easy-cast"
+version = "0.5.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "10936778145f3bea71fd9bf61332cce28c28e96a380714f7ab34838b80733fd6"
+dependencies = [
+ "libm",
+]
+
+[[package]]
+name = "either"
+version = "1.12.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3dca9240753cf90908d7e4aac30f630662b02aebaa1b58a3cadabdb23385b58b"
+
+[[package]]
+name = "encode_unicode"
+version = "0.3.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f"
+
+[[package]]
+name = "encode_unicode"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "34aa73646ffb006b8f5147f3dc182bd4bcb190227ce861fc4a4844bf8e3cb2c0"
+
+[[package]]
+name = "env_logger"
+version = "0.10.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580"
+dependencies = [
+ "humantime",
+ "is-terminal",
+ "log",
+ "regex",
+ "termcolor",
+]
+
+[[package]]
+name = "equivalent"
+version = "1.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
+
+[[package]]
+name = "fallible-iterator"
+version = "0.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2acce4a10f12dc2fb14a218589d4f1f62ef011b2d0cc4b3cb1bba8e94da14649"
+
+[[package]]
+name = "fallible-streaming-iterator"
+version = "0.1.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7360491ce676a36bf9bb3c56c1aa791658183a54d2744120f27285738d90465a"
+
+[[package]]
+name = "flate2"
+version = "1.0.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae"
+dependencies = [
+ "crc32fast",
+ "miniz_oxide",
+]
+
+[[package]]
+name = "float-ord"
+version = "0.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8ce81f49ae8a0482e4c55ea62ebbd7e5a686af544c00b9d090bba3ff9be97b3d"
+
+[[package]]
+name = "form_urlencoded"
+version = "1.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e13624c2627564efccf4934284bdd98cbaa14e79b0b5a141218e507b3a823456"
+dependencies = [
+ "percent-encoding",
+]
+
+[[package]]
+name = "fs-utils"
+version = "1.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6fc7a9dc005c944c98a935e7fd626faf5bf7e5a609f94bc13e42fc4a02e52593"
+dependencies = [
+ "quick-error",
+]
+
+[[package]]
+name = "getrandom"
+version = "0.2.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94b22e06ecb0110981051723910cbf0b5f5e09a2062dd7663334ee79a9d1286c"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "wasi",
+]
+
+[[package]]
+name = "glob"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
+
+[[package]]
+name = "half"
+version = "2.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888"
+dependencies = [
+ "cfg-if",
+ "crunchy",
+]
+
+[[package]]
+name = "hashbrown"
+version = "0.14.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
+dependencies = [
+ "ahash",
+ "allocator-api2",
+ "rayon",
+ "serde",
+]
+
+[[package]]
+name = "hashlink"
+version = "0.8.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e8094feaf31ff591f651a2664fb9cfd92bba7a60ce3197265e9482ebe753c8f7"
+dependencies = [
+ "hashbrown",
+]
+
+[[package]]
+name = "heck"
+version = "0.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
+
+[[package]]
+name = "heck"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
+
+[[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 = [
+ "bzip2-sys",
+ "cc",
+ "curl-sys",
+ "fs-utils",
+ "glob",
+ "libz-sys",
+ "lzma-sys",
+ "openssl-sys",
+]
+
+[[package]]
+name = "humantime"
+version = "2.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4"
+
+[[package]]
+name = "idna"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "634d9b1461af396cad843f47fdba5597a4f9e6ddd4bfb6ff5d85028c25cb12f6"
+dependencies = [
+ "unicode-bidi",
+ "unicode-normalization",
+]
+
+[[package]]
+name = "ieee754"
+version = "0.2.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c"
+
+[[package]]
+name = "indexmap"
+version = "2.2.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26"
+dependencies = [
+ "equivalent",
+ "hashbrown",
+]
+
+[[package]]
+name = "indicatif"
+version = "0.17.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "763a5a8f45087d6bcea4222e7b72c291a054edf80e4ef6efd2a4979878c7bea3"
+dependencies = [
+ "console",
+ "instant",
+ "number_prefix",
+ "portable-atomic",
+ "rayon",
+ "unicode-width",
+]
+
+[[package]]
+name = "indicatif-log-bridge"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2963046f28a204e3e3fd7e754fd90a6235da05b5378f24707ff0ec9513725ce3"
+dependencies = [
+ "indicatif",
+ "log",
+]
+
+[[package]]
+name = "instant"
+version = "0.1.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c"
+dependencies = [
+ "cfg-if",
+]
+
+[[package]]
+name = "is-terminal"
+version = "0.4.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b"
+dependencies = [
+ "hermit-abi",
+ "libc",
+ "windows-sys",
+]
+
+[[package]]
+name = "is_terminal_polyfill"
+version = "1.70.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800"
+
+[[package]]
+name = "itertools"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569"
+dependencies = [
+ "either",
+]
+
+[[package]]
+name = "itoa"
+version = "1.0.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b"
+
+[[package]]
+name = "jobserver"
+version = "0.1.31"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d2b099aaa34a9751c5bf0878add70444e1ed2dd73f347be99003d4577277de6e"
+dependencies = [
+ "libc",
+]
+
+[[package]]
+name = "lazy_static"
+version = "1.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
+
+[[package]]
+name = "lexical-core"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2cde5de06e8d4c2faabc400238f9ae1c74d5412d03a7bd067645ccbc47070e46"
+dependencies = [
+ "lexical-parse-float",
+ "lexical-parse-integer",
+ "lexical-util",
+ "lexical-write-float",
+ "lexical-write-integer",
+]
+
+[[package]]
+name = "lexical-parse-float"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "683b3a5ebd0130b8fb52ba0bdc718cc56815b6a097e28ae5a6997d0ad17dc05f"
+dependencies = [
+ "lexical-parse-integer",
+ "lexical-util",
+ "static_assertions",
+]
+
+[[package]]
+name = "lexical-parse-integer"
+version = "0.8.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6d0994485ed0c312f6d965766754ea177d07f9c00c9b82a5ee62ed5b47945ee9"
+dependencies = [
+ "lexical-util",
+ "static_assertions",
+]
+
+[[package]]
+name = "lexical-util"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5255b9ff16ff898710eb9eb63cb39248ea8a5bb036bea8085b1a767ff6c4e3fc"
+dependencies = [
+ "static_assertions",
+]
+
+[[package]]
+name = "lexical-write-float"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "accabaa1c4581f05a3923d1b4cfd124c329352288b7b9da09e766b0668116862"
+dependencies = [
+ "lexical-util",
+ "lexical-write-integer",
+ "static_assertions",
+]
+
+[[package]]
+name = "lexical-write-integer"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e1b6f3d1f4422866b68192d62f77bc5c700bee84f3069f2469d7bc8c77852446"
+dependencies = [
+ "lexical-util",
+ "static_assertions",
+]
+
+[[package]]
+name = "libc"
+version = "0.2.153"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
+
+[[package]]
+name = "libm"
+version = "0.2.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
+
+[[package]]
+name = "libredox"
+version = "0.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c0ff37bd590ca25063e35af745c343cb7a0271906fb7b37e4813e8f79f00268d"
+dependencies = [
+ "bitflags",
+ "libc",
+]
+
+[[package]]
+name = "libsqlite3-sys"
+version = "0.27.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cf4e226dcd58b4be396f7bd3c20da8fdee2911400705297ba7d2d7cc2c30f716"
+dependencies = [
+ "pkg-config",
+ "vcpkg",
+]
+
+[[package]]
+name = "libz-sys"
+version = "1.1.16"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5e143b5e666b2695d28f6bca6497720813f699c9602dd7f5cac91008b8ada7f9"
+dependencies = [
+ "cc",
+ "cmake",
+ "libc",
+ "pkg-config",
+ "vcpkg",
+]
+
+[[package]]
+name = "linear-map"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
+
+[[package]]
+name = "lock_api"
+version = "0.4.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17"
+dependencies = [
+ "autocfg",
+ "scopeguard",
+]
+
+[[package]]
+name = "log"
+version = "0.4.21"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "90ed8c1e510134f979dbc4f070f87d4313098b704861a105fe34231c70a3901c"
+
+[[package]]
+name = "lzma-sys"
+version = "0.1.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27"
+dependencies = [
+ "cc",
+ "libc",
+ "pkg-config",
+]
+
+[[package]]
+name = "matrixmultiply"
+version = "0.3.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7574c1cf36da4798ab73da5b215bbf444f50718207754cb522201d78d1cd0ff2"
+dependencies = [
+ "autocfg",
+ "rawpointer",
+]
+
+[[package]]
+name = "memchr"
+version = "2.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
+
+[[package]]
+name = "miniz_oxide"
+version = "0.7.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7"
+dependencies = [
+ "adler",
+]
+
+[[package]]
+name = "nalgebra"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d506eb7e08d6329505faa8a3a00a5dcc6de9f76e0c77e4b75763ae3c770831ff"
+dependencies = [
+ "approx",
+ "matrixmultiply",
+ "nalgebra-macros",
+ "num-complex",
+ "num-rational",
+ "num-traits",
+ "rand",
+ "rand_distr",
+ "simba",
+ "typenum",
+]
+
+[[package]]
+name = "nalgebra-macros"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "01fcc0b8149b4632adc89ac3b7b31a12fb6099a0317a4eb2ebff574ef7de7218"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 1.0.109",
+]
+
+[[package]]
+name = "newtype_derive"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec"
+dependencies = [
+ "rustc_version",
+]
+
+[[package]]
+name = "noodles-bam"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7e75824c4fad4713c177148543d96893212c2b8b6efc3cd9fc19934bb9334c97"
+dependencies = [
+ "bit-vec",
+ "byteorder",
+ "bytes",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core 0.13.0",
+ "noodles-csi 0.29.0",
+ "noodles-sam",
+]
+
+[[package]]
+name = "noodles-bgzf"
+version = "0.26.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8970db2e84adb1007377dd3988258d7a64e3fc4c05602ebf94e1f8cba207c030"
+dependencies = [
+ "byteorder",
+ "bytes",
+ "crossbeam-channel",
+ "flate2",
+]
+
+[[package]]
+name = "noodles-core"
+version = "0.13.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2993a01927b449e191670446b8a36e153e89fc4527a246a84eed9057adeefe1b"
+
+[[package]]
+name = "noodles-core"
+version = "0.14.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7336c3be652de4e05444c9b12a32331beb5ba3316e8872d92bfdd8ef3b06c282"
+
+[[package]]
+name = "noodles-csi"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9abd5616c374ad3da6677603dc1637ef518388537ec4a0263b8e4471ee5b0801"
+dependencies = [
+ "bit-vec",
+ "byteorder",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core 0.13.0",
+]
+
+[[package]]
+name = "noodles-csi"
+version = "0.30.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a60dfe0919f7ecbd081a82eb1d32e8f89f9041932d035fe8309073c8c01277bf"
+dependencies = [
+ "bit-vec",
+ "byteorder",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core 0.14.0",
+]
+
+[[package]]
+name = "noodles-fasta"
+version = "0.33.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5e9e953e4e90e6c96e6a384598ebf2ab6d2f5add259ff05a194cf635e892c980"
+dependencies = [
+ "bytes",
+ "memchr",
+ "noodles-bgzf",
+ "noodles-core 0.14.0",
+]
+
+[[package]]
+name = "noodles-gff"
+version = "0.27.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "14f8ec87fe3630f57d6d8ea24cbc2cbd0bfed1fe66238bda7a7c3fb6a36d3713"
+dependencies = [
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core 0.14.0",
+ "noodles-csi 0.30.0",
+ "percent-encoding",
+]
+
+[[package]]
+name = "noodles-sam"
+version = "0.49.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2b94966806ac7aec118d41eea7080bfbd0e8b843ba64f46522c57f0f55cfb1f0"
+dependencies = [
+ "bitflags",
+ "indexmap",
+ "lexical-core",
+ "memchr",
+ "noodles-bgzf",
+ "noodles-core 0.13.0",
+ "noodles-csi 0.29.0",
+]
+
+[[package]]
+name = "noodles-tabix"
+version = "0.36.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cc1ab29335a68d0c2bdf41460a67714ca69e23a1cbeb950ac5c38a9afa446a62"
+dependencies = [
+ "bit-vec",
+ "byteorder",
+ "indexmap",
+ "noodles-bgzf",
+ "noodles-core 0.14.0",
+ "noodles-csi 0.30.0",
+]
+
+[[package]]
+name = "noodles-vcf"
+version = "0.49.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2e1f2fa749afaccadc596ec55ccb7bdcd8101fa79f8382384223c0dbae3e245b"
+dependencies = [
+ "indexmap",
+ "memchr",
+ "noodles-bgzf",
+ "noodles-core 0.14.0",
+ "noodles-csi 0.30.0",
+ "noodles-tabix",
+ "percent-encoding",
+]
+
+[[package]]
+name = "num-complex"
+version = "0.4.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495"
+dependencies = [
+ "num-traits",
+]
+
+[[package]]
+name = "num-integer"
+version = "0.1.46"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f"
+dependencies = [
+ "num-traits",
+]
+
+[[package]]
+name = "num-rational"
+version = "0.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f83d14da390562dca69fc84082e73e548e1ad308d24accdedd2720017cb37824"
+dependencies = [
+ "num-integer",
+ "num-traits",
+]
+
+[[package]]
+name = "num-traits"
+version = "0.2.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841"
+dependencies = [
+ "autocfg",
+ "libm",
+]
+
+[[package]]
+name = "number_prefix"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
+
+[[package]]
+name = "once_cell"
+version = "1.19.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
+
+[[package]]
+name = "openssl-src"
+version = "300.2.3+3.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5cff92b6f71555b61bb9315f7c64da3ca43d87531622120fea0195fc761b4843"
+dependencies = [
+ "cc",
+]
+
+[[package]]
+name = "openssl-sys"
+version = "0.9.102"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c597637d56fbc83893a35eb0dd04b2b8e7a50c91e64e9493e398b5df4fb45fa2"
+dependencies = [
+ "cc",
+ "libc",
+ "openssl-src",
+ "pkg-config",
+ "vcpkg",
+]
+
+[[package]]
+name = "pandora_lib_case"
+version = "0.1.0"
+dependencies = [
+ "anyhow",
+ "clap",
+ "confy",
+ "env_logger",
+ "glob",
+ "indicatif",
+ "indicatif-log-bridge",
+ "itertools",
+ "log",
+ "pandora_lib_pileup",
+ "pandora_lib_report",
+ "pandora_lib_stats",
+ "pandora_lib_variants",
+ "rand",
+ "rayon",
+ "rust-htslib 0.46.0",
+ "serde",
+]
+
+[[package]]
+name = "pandora_lib_pileup"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_pileup.git#7ad13b0f8811a1676acae0331b6e04e01dc1d411"
+dependencies = [
+ "anyhow",
+ "average",
+ "env_logger",
+ "log",
+ "rayon",
+ "rust-htslib 0.46.0",
+]
+
+[[package]]
+name = "pandora_lib_report"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_report.git#39476082bc62b27dec6de017ad741044833d7d47"
+dependencies = [
+ "crossbeam",
+ "indicatif",
+]
+
+[[package]]
+name = "pandora_lib_stats"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_stats.git#a453d2ee70b77125ed4c2225acd0ef22786652aa"
+dependencies = [
+ "anyhow",
+ "statrs",
+]
+
+[[package]]
+name = "pandora_lib_variants"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_variants.git#53cbd13629ece9d4612dffd2a58d8c4f208b5fbf"
+dependencies = [
+ "anyhow",
+ "bgzip",
+ "clap",
+ "confy",
+ "crossbeam-deque",
+ "csv",
+ "dashmap",
+ "env_logger",
+ "hashbrown",
+ "indicatif",
+ "indicatif-log-bridge",
+ "log",
+ "noodles-bam",
+ "noodles-bgzf",
+ "noodles-core 0.14.0",
+ "noodles-csi 0.30.0",
+ "noodles-fasta",
+ "noodles-gff",
+ "noodles-sam",
+ "noodles-tabix",
+ "noodles-vcf",
+ "num-integer",
+ "pot",
+ "prettytable-rs",
+ "rayon",
+ "rust-htslib 0.44.1",
+ "rust-lapper",
+ "serde",
+ "serde_json",
+ "serde_rusqlite",
+ "statrs",
+ "trc",
+ "uuid",
+]
+
+[[package]]
+name = "parking_lot_core"
+version = "0.9.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "redox_syscall",
+ "smallvec",
+ "windows-targets",
+]
+
+[[package]]
+name = "paste"
+version = "1.0.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a"
+
+[[package]]
+name = "percent-encoding"
+version = "2.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e"
+
+[[package]]
+name = "pkg-config"
+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec"
+
+[[package]]
+name = "portable-atomic"
+version = "1.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0"
+
+[[package]]
+name = "pot"
+version = "3.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "df842bdb3b0553a411589e64aaa1a7d0c0259f72fabcedfaa841683ae3019d80"
+dependencies = [
+ "byteorder",
+ "half",
+ "serde",
+]
+
+[[package]]
+name = "ppv-lite86"
+version = "0.2.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
+
+[[package]]
+name = "prettytable-rs"
+version = "0.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "eea25e07510aa6ab6547308ebe3c036016d162b8da920dbb079e3ba8acf3d95a"
+dependencies = [
+ "csv",
+ "encode_unicode 1.0.0",
+ "is-terminal",
+ "lazy_static",
+ "term",
+ "unicode-width",
+]
+
+[[package]]
+name = "proc-macro2"
+version = "1.0.82"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8ad3d49ab951a01fbaafe34f2ec74122942fe18a3f9814c3268f1bb72042131b"
+dependencies = [
+ "unicode-ident",
+]
+
+[[package]]
+name = "quick-error"
+version = "1.2.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
+
+[[package]]
+name = "quote"
+version = "1.0.36"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
+dependencies = [
+ "proc-macro2",
+]
+
+[[package]]
+name = "rand"
+version = "0.8.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404"
+dependencies = [
+ "libc",
+ "rand_chacha",
+ "rand_core",
+]
+
+[[package]]
+name = "rand_chacha"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88"
+dependencies = [
+ "ppv-lite86",
+ "rand_core",
+]
+
+[[package]]
+name = "rand_core"
+version = "0.6.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c"
+dependencies = [
+ "getrandom",
+]
+
+[[package]]
+name = "rand_distr"
+version = "0.4.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "32cb0b9bc82b0a0876c2dd994a7e7a2683d3e7390ca40e6886785ef0c7e3ee31"
+dependencies = [
+ "num-traits",
+ "rand",
+]
+
+[[package]]
+name = "rawpointer"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
+
+[[package]]
+name = "rayon"
+version = "1.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa"
+dependencies = [
+ "either",
+ "rayon-core",
+]
+
+[[package]]
+name = "rayon-core"
+version = "1.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2"
+dependencies = [
+ "crossbeam-deque",
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "redox_syscall"
+version = "0.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "469052894dcb553421e483e4209ee581a45100d31b4018de03e5a7ad86374a7e"
+dependencies = [
+ "bitflags",
+]
+
+[[package]]
+name = "redox_users"
+version = "0.4.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bd283d9651eeda4b2a83a43c1c91b266c40fd76ecd39a50a8c630ae69dc72891"
+dependencies = [
+ "getrandom",
+ "libredox",
+ "thiserror",
+]
+
+[[package]]
+name = "regex"
+version = "1.10.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c"
+dependencies = [
+ "aho-corasick",
+ "memchr",
+ "regex-automata",
+ "regex-syntax",
+]
+
+[[package]]
+name = "regex-automata"
+version = "0.4.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea"
+dependencies = [
+ "aho-corasick",
+ "memchr",
+ "regex-syntax",
+]
+
+[[package]]
+name = "regex-syntax"
+version = "0.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56"
+
+[[package]]
+name = "rusqlite"
+version = "0.30.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a78046161564f5e7cd9008aff3b2990b3850dc8e0349119b98e8f251e099f24d"
+dependencies = [
+ "bitflags",
+ "fallible-iterator",
+ "fallible-streaming-iterator",
+ "hashlink",
+ "libsqlite3-sys",
+ "smallvec",
+]
+
+[[package]]
+name = "rust-htslib"
+version = "0.44.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7c7eb0f29fce64a4e22578905efef3d72389058016023279a58b282eb5c0c467"
+dependencies = [
+ "bio-types",
+ "byteorder",
+ "custom_derive",
+ "derive-new",
+ "hts-sys",
+ "ieee754",
+ "lazy_static",
+ "libc",
+ "linear-map",
+ "newtype_derive",
+ "regex",
+ "thiserror",
+ "url",
+]
+
+[[package]]
+name = "rust-htslib"
+version = "0.46.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "aec6f9ca4601beb4ae75ff8c99144dd15de5a873f6adf058da299962c760968e"
+dependencies = [
+ "bio-types",
+ "byteorder",
+ "custom_derive",
+ "derive-new",
+ "hts-sys",
+ "ieee754",
+ "lazy_static",
+ "libc",
+ "libz-sys",
+ "linear-map",
+ "newtype_derive",
+ "regex",
+ "thiserror",
+ "url",
+]
+
+[[package]]
+name = "rust-lapper"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ee43d8e721ac803031dbab6a944b957b49a3b11eadbc099880c8aaaebf23ed27"
+dependencies = [
+ "num-traits",
+]
+
+[[package]]
+name = "rustc_version"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084"
+dependencies = [
+ "semver",
+]
+
+[[package]]
+name = "rustversion"
+version = "1.0.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "955d28af4278de8121b7ebeb796b6a45735dc01436d898801014aced2773a3d6"
+
+[[package]]
+name = "ryu"
+version = "1.0.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
+
+[[package]]
+name = "safe_arch"
+version = "0.7.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f398075ce1e6a179b46f51bd88d0598b92b00d3551f1a2d4ac49e771b56ac354"
+dependencies = [
+ "bytemuck",
+]
+
+[[package]]
+name = "scopeguard"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
+
+[[package]]
+name = "semver"
+version = "0.1.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
+
+[[package]]
+name = "serde"
+version = "1.0.202"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "226b61a0d411b2ba5ff6d7f73a476ac4f8bb900373459cd00fab8512828ba395"
+dependencies = [
+ "serde_derive",
+]
+
+[[package]]
+name = "serde_derive"
+version = "1.0.202"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6048858004bcff69094cd972ed40a32500f153bd3be9f716b2eed2e8217c4838"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.64",
+]
+
+[[package]]
+name = "serde_json"
+version = "1.0.117"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "455182ea6142b14f93f4bc5320a2b31c1f266b66a4a5c858b013302a5d8cbfc3"
+dependencies = [
+ "itoa",
+ "ryu",
+ "serde",
+]
+
+[[package]]
+name = "serde_rusqlite"
+version = "0.34.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4600dac14aada464c5584d327baa164e372153309bc4c0fb1498bbfbaa5a028b"
+dependencies = [
+ "rusqlite",
+ "serde",
+]
+
+[[package]]
+name = "simba"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f0b7840f121a46d63066ee7a99fc81dcabbc6105e437cae43528cea199b5a05f"
+dependencies = [
+ "approx",
+ "num-complex",
+ "num-traits",
+ "paste",
+ "wide",
+]
+
+[[package]]
+name = "smallvec"
+version = "1.13.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
+
+[[package]]
+name = "stable_deref_trait"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a8f112729512f8e442d81f95a8a7ddf2b7c6b8a1a6f509a95864142b30cab2d3"
+
+[[package]]
+name = "static_assertions"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
+
+[[package]]
+name = "statrs"
+version = "0.16.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2d08e5e1748192713cc281da8b16924fb46be7b0c2431854eadc785823e5696e"
+dependencies = [
+ "approx",
+ "lazy_static",
+ "nalgebra",
+ "num-traits",
+ "rand",
+]
+
+[[package]]
+name = "strsim"
+version = "0.11.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
+
+[[package]]
+name = "strum_macros"
+version = "0.25.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "23dc1fa9ac9c169a78ba62f0b841814b7abae11bdd047b9c58f893439e309ea0"
+dependencies = [
+ "heck 0.4.1",
+ "proc-macro2",
+ "quote",
+ "rustversion",
+ "syn 2.0.64",
+]
+
+[[package]]
+name = "syn"
+version = "1.0.109"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "syn"
+version = "2.0.64"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7ad3dee41f36859875573074334c200d1add8e4a87bb37113ebd31d926b7b11f"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "term"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c59df8ac95d96ff9bede18eb7300b0fda5e5d8d90960e76f8e14ae765eedbf1f"
+dependencies = [
+ "dirs-next",
+ "rustversion",
+ "winapi",
+]
+
+[[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"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "579e9083ca58dd9dcf91a9923bb9054071b9ebbd800b342194c9feb0ee89fc18"
+dependencies = [
+ "thiserror-impl",
+]
+
+[[package]]
+name = "thiserror-impl"
+version = "1.0.60"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e2470041c06ec3ac1ab38d0356a6119054dedaea53e12fbefc0de730a1c08524"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.64",
+]
+
+[[package]]
+name = "tinyvec"
+version = "1.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+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"
+version = "0.5.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f4f7f0dd8d50a853a531c426359045b1998f04219d88799810762cd4ad314234"
+dependencies = [
+ "serde",
+]
+
+[[package]]
+name = "trc"
+version = "1.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "91dd8e922a6b95b816407eb8c37e17a409512f759561ac48ec2b7281b395a3c6"
+dependencies = [
+ "serde",
+ "stable_deref_trait",
+]
+
+[[package]]
+name = "typenum"
+version = "1.17.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
+
+[[package]]
+name = "unicode-bidi"
+version = "0.3.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "08f95100a766bf4f8f28f90d77e0a5461bbdb219042e7679bebe79004fed8d75"
+
+[[package]]
+name = "unicode-ident"
+version = "1.0.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
+
+[[package]]
+name = "unicode-normalization"
+version = "0.1.23"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a56d1686db2308d901306f92a263857ef59ea39678a5458e7cb17f01415101f5"
+dependencies = [
+ "tinyvec",
+]
+
+[[package]]
+name = "unicode-width"
+version = "0.1.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68f5e5f3158ecfd4b8ff6fe086db7c8467a2dfdac97fe420f2b7c4aa97af66d6"
+
+[[package]]
+name = "url"
+version = "2.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "31e6302e3bb753d46e83516cae55ae196fc0c309407cf11ab35cc51a4c2a4633"
+dependencies = [
+ "form_urlencoded",
+ "idna",
+ "percent-encoding",
+]
+
+[[package]]
+name = "utf8parse"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
+
+[[package]]
+name = "uuid"
+version = "1.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a183cf7feeba97b4dd1c0d46788634f6221d87fa961b305bed08c851829efcc0"
+dependencies = [
+ "getrandom",
+ "serde",
+]
+
+[[package]]
+name = "vcpkg"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
+
+[[package]]
+name = "version_check"
+version = "0.9.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
+
+[[package]]
+name = "wasi"
+version = "0.11.0+wasi-snapshot-preview1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
+
+[[package]]
+name = "wide"
+version = "0.7.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "aab6594190de06d718a5dbc5fa781ab62f8903797056480e549ca74add6b7065"
+dependencies = [
+ "bytemuck",
+ "safe_arch",
+]
+
+[[package]]
+name = "winapi"
+version = "0.3.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
+dependencies = [
+ "winapi-i686-pc-windows-gnu",
+ "winapi-x86_64-pc-windows-gnu",
+]
+
+[[package]]
+name = "winapi-i686-pc-windows-gnu"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
+
+[[package]]
+name = "winapi-util"
+version = "0.1.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
+dependencies = [
+ "windows-sys",
+]
+
+[[package]]
+name = "winapi-x86_64-pc-windows-gnu"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"
+
+[[package]]
+name = "windows-sys"
+version = "0.52.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
+dependencies = [
+ "windows-targets",
+]
+
+[[package]]
+name = "windows-targets"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb"
+dependencies = [
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
+]
+
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263"
+
+[[package]]
+name = "windows_aarch64_msvc"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6"
+
+[[package]]
+name = "windows_i686_gnu"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670"
+
+[[package]]
+name = "windows_i686_gnullvm"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9"
+
+[[package]]
+name = "windows_i686_msvc"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf"
+
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9"
+
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596"
+
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.52.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0"
+
+[[package]]
+name = "zerocopy"
+version = "0.7.34"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ae87e3fcd617500e5d106f0380cf7b77f3c6092aae37191433159dda23cfb087"
+dependencies = [
+ "zerocopy-derive",
+]
+
+[[package]]
+name = "zerocopy-derive"
+version = "0.7.34"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.64",
+]

Cargo.toml

@@ -0,0 +1,25 @@
+[package]
+name = "pandora_lib_case"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+log = "^0.4.20"
+env_logger = "^0.10.1"
+clap = { version = "^4.3.16", features = ["derive"] }
+anyhow = "^1.0.75"
+serde = { version = "^1.0.188", features = ["derive"] }
+pandora_lib_variants = { git = "https://git.t0m4.fr/Thomas/pandora_lib_variants.git" }
+pandora_lib_report = { git = "https://git.t0m4.fr/Thomas/pandora_lib_report.git" }
+pandora_lib_pileup = { git = "https://git.t0m4.fr/Thomas/pandora_lib_pileup.git" }
+pandora_lib_stats = { git = "https://git.t0m4.fr/Thomas/pandora_lib_stats.git" }
+indicatif = "0.17.8"
+glob = "0.3.1"
+confy = "0.5.1"
+rust-htslib = "0.46.0"
+itertools = "0.12.1"
+indicatif-log-bridge = "0.2.2"
+rand = "0.8.5"
+rayon = "1.10.0"

src/bam.rs

@@ -0,0 +1,39 @@
+use std::{collections::HashSet, path::PathBuf};
+use itertools::Itertools;
+
+use anyhow::{Context, Error, Ok, Result, anyhow};
+use rust_htslib::{bam, bam::Read};
+
+#[derive(Debug, Clone)]
+pub struct Bam {
+    pub path: PathBuf,
+    pub origin: BamOrigin,
+}
+
+#[derive(Debug, Clone)]
+pub enum BamOrigin {
+    DIAG,
+    MRD,
+}
+
+impl Bam {
+    pub fn new(path: PathBuf, origin: BamOrigin) -> Self {
+        Self { path, origin }
+    }
+
+    pub fn get_composition(&self, n: usize) -> Result<Vec<(String, f64)>> {
+        let mut bam = bam::Reader::from_path(self.path.to_str().unwrap()).unwrap();
+
+        let mut rgs = Vec::new();
+        for r in bam.records().take(n) {
+            let record = r.unwrap();
+            match record.aux("RG".as_bytes()).context("Can't access RG tag.")? {
+                bam::record::Aux::String(s) => rgs.push(s.to_string()),
+                _ => (),
+            };
+        }
+        Ok(rgs.into_iter().counts().into_iter().map(|(rg, size)| {
+            (rg, size as f64 / n as f64)
+        }).collect())
+    }
+}

src/cases.rs

@@ -0,0 +1,294 @@
+use crate::{
+    bam::{Bam, BamOrigin},
+    config::Config,
+};
+use anyhow::{Context, Ok, Result};
+use glob::glob;
+use indicatif::MultiProgress;
+use itertools::Itertools;
+use log::{info, warn};
+use pandora_lib_pileup::get_hts_nt_pileup;
+use pandora_lib_stats::chi_square_test_for_proportions;
+use pandora_lib_variants::variants::*;
+use rayon::prelude::*;
+use std::{
+    collections::HashMap,
+    io::{BufRead, BufReader},
+    ops::{Deref, DerefMut},
+    path::Path,
+    sync::{Arc, Mutex},
+};
+use rand::seq::IteratorRandom;
+use rust_htslib::bam;
+
+#[derive(Debug)]
+pub struct Cases {
+    pub cases: Vec<Case>,
+    pub config: Config,
+}
+
+impl Cases {
+    pub fn load(mp: MultiProgress) -> Result<Self> {
+        let config = Config::get()?;
+        let mut diag_bams = HashMap::new();
+        for entry in glob(&config.diag_bam_glob).context("Failed to read glob pattern")? {
+            let path = entry?;
+            let case_id = path
+                .parent()
+                .context("")?
+                .parent()
+                .context("")?
+                .file_name()
+                .context("")?
+                .to_str()
+                .context("")?
+                .to_string();
+
+            let b = Bam::new(path.clone(), BamOrigin::DIAG);
+            diag_bams.insert(case_id, b);
+        }
+
+        let mut mrd_bams = HashMap::new();
+        for entry in glob(&config.mrd_bam_glob).context("Failed to read glob pattern")? {
+            let path = entry?;
+            let case_id = path
+                .parent()
+                .context("")?
+                .parent()
+                .context("")?
+                .file_name()
+                .context("")?
+                .to_str()
+                .context("")?
+                .to_string();
+
+            let b = Bam::new(path.clone(), BamOrigin::MRD);
+            mrd_bams.insert(case_id, b);
+        }
+
+        let mut cases = Vec::new();
+        let diff_snp = DiffSnp::init(&config.commun_snp)?;
+        for (id, diag_bam) in diag_bams {
+            if let Some(mrd_bam) = mrd_bams.get(&id) {
+                // verify if both samples match commun snps
+                let diff = diff_snp.diff_prop(diag_bam.path.to_str().unwrap(), mrd_bam.path.to_str().unwrap())?;
+
+                if diff < config.max_snp_diff_prop {
+                    let mut case = Case::new(id.clone(), diag_bam.clone(), mrd_bam.clone())?;
+                    let dir = diag_bam.path.parent().context("")?.to_str().context("")?;
+                    case.load_variants(&format!("{dir}/{id}_variants.bytes.gz"), &mp)?;
+                    cases.push(case);
+                } else {
+                    warn!("{id} diag and mrd seems to have been sequenced from two patients.");
+                }
+            }
+        }
+        Ok(Self { cases, config })
+    }
+
+    pub fn stats(&self) {
+        self.iter().for_each(|case| {
+            let n_var = match case.n_variants() {
+                Some(n) => n.to_string(),
+                None => "NA".to_string(),
+            };
+            let cols = vec![case.id.to_string(), n_var];
+            info!("{}", cols.join("\t"));
+        })
+    }
+}
+
+impl IntoIterator for Cases {
+    type Item = Case;
+    type IntoIter = <Vec<Case> as IntoIterator>::IntoIter; // so that you don't have to write std::vec::IntoIter, which nobody remembers anyway
+
+    fn into_iter(self) -> Self::IntoIter {
+        self.cases.into_iter()
+    }
+}
+
+impl Deref for Cases {
+    type Target = Vec<Case>;
+
+    fn deref(&self) -> &Self::Target {
+        &self.cases
+    }
+}
+
+impl DerefMut for Cases {
+    fn deref_mut(&mut self) -> &mut Vec<Case> {
+        &mut self.cases
+    }
+}
+
+#[derive(Debug)]
+pub struct Case {
+    pub id: String,
+    pub diag_bam: Bam,
+    pub mrd_bam: Bam,
+    pub variants: Option<Variants>,
+}
+
+impl Case {
+    pub fn new(id: String, diag_bam: Bam, mrd_bam: Bam) -> Result<Self> {
+        Ok(Self {
+            id,
+            diag_bam,
+            mrd_bam,
+            variants: None,
+        })
+    }
+    pub fn load_variants(&mut self, variants_path: &str, mp: &MultiProgress) -> Result<()> {
+        info!("Loading variants for {}", self.id);
+        if !Path::new(variants_path).exists() {
+            match run_pipe(&self.id, &mp) {
+                std::result::Result::Ok(_) => info!("{} variants analyzed.", self.id),
+                Err(e) => warn!("Error while analyzing {}: {e}", self.id),
+            }
+        }
+        if let std::result::Result::Ok(variants) =
+            Variants::new_from_bytes(&self.id, variants_path, mp.clone())
+        {
+            self.variants = Some(variants);
+        }
+
+        Ok(())
+    }
+    pub fn n_variants(&self) -> Option<usize> {
+        match &self.variants {
+            Some(v) => Some(v.len()),
+            None => None,
+        }
+    }
+}
+
+pub struct DiffSnp {
+    lines: Vec<String>,
+}
+
+impl DiffSnp {
+    pub fn init(commun_snp: &str) -> Result<Self> {
+        info!("Loading {commun_snp}");
+        let commun_snp_reader =
+            BufReader::new(pandora_lib_variants::in_out::get_reader(commun_snp)?);
+        let lines: Vec<String> = commun_snp_reader
+            .lines()
+            .into_iter()
+            .map(|e| e.unwrap())
+            .collect();
+        Ok(Self { lines })
+    }
+
+    pub fn diff_prop(&self, diag_bam_path: &str, mrd_bam_path: &str) -> Result<f64> {
+        let mut rng = rand::thread_rng();
+        let lines = self.lines.clone().into_iter().choose_multiple(&mut rng, 10_000);
+        let max_p_val = 0.0001;
+        let diff = Arc::new(Mutex::new(0u64));
+        let eq = Arc::new(Mutex::new(0u64));
+        lines.par_chunks(100).for_each(|snp_lines| {
+            let mut diag_bam = bam::IndexedReader::from_path(diag_bam_path).unwrap();
+            let mut mrd_bam = bam::IndexedReader::from_path(mrd_bam_path).unwrap();
+
+            for snp_line in snp_lines.iter() {
+                let snp_cols: Vec<&str> = snp_line.splitn(3, "\t").collect();
+                let diag_pileup = get_hts_nt_pileup(
+                    &mut diag_bam,
+                    snp_cols.get(0).unwrap(),
+                    snp_cols[1].parse().unwrap(),
+                    false,
+                )
+                .unwrap();
+                let diag_pileup_counts: Vec<_> = diag_pileup
+                    .clone()
+                    .into_iter()
+                    .counts()
+                    .into_iter()
+                    .filter(|(b, _)| *b != b'D')
+                    .filter(|(_, n)| *n > 2)
+                    .collect();
+                let diag_pileup_len = diag_pileup.len();
+                if diag_pileup_len >= 10 && diag_pileup_counts.len() <= 2 {
+                    let mrd_pileup = get_hts_nt_pileup(
+                        &mut mrd_bam,
+                        snp_cols[0],
+                        snp_cols[1].parse().unwrap(),
+                        false,
+                    )
+                    .unwrap();
+                    let mrd_pileup_len = mrd_pileup.len();
+                    let mrd_pileup_counts: Vec<_> = mrd_pileup
+                        .clone()
+                        .into_iter()
+                        .counts()
+                        .into_iter()
+                        .filter(|(b, _)| *b != b'D')
+                        .filter(|(_, n)| *n > 2)
+                        .collect();
+
+                    if mrd_pileup_len >= 10 && mrd_pileup_counts.len() <= 2 {
+                        if mrd_pileup_counts.len() == 1 && diag_pileup_counts.len() == 1 {
+                            let (diag_a_b, _) = diag_pileup_counts.first().unwrap();
+                            let (mrd_a_b, _) = diag_pileup_counts.first().unwrap();
+
+                            if diag_a_b != mrd_a_b {
+                                // println!("diff {snp_cols:?}");
+                                let mut d = diff.lock().unwrap();
+                                *d += 1;
+                            } else {
+                                // println!("eq {snp_cols:?}");
+                                let mut e = eq.lock().unwrap();
+                                *e += 1;
+                            }
+                        } else if mrd_pileup_counts.len() != diag_pileup_counts.len() {
+                            // println!("diff {snp_cols:?} {mrd_pileup_counts:?} {diag_pileup_counts:?}");
+                            let mut d = diff.lock().unwrap();
+                            *d += 1;
+                            // let mut d = diff.lock().unwrap();
+                            // *d += 1;
+                        } else if mrd_pileup_counts.len() == 2 && diag_pileup_counts.len() == 2 {
+                            let (diag_a_b, diag_a_n) = diag_pileup_counts.first().unwrap();
+                            let (diag_b_b, diag_b_n) = diag_pileup_counts.last().unwrap();
+                            let (mrd_a_b, mrd_a_n) = diag_pileup_counts.first().unwrap();
+
+                            let (a, c) = if diag_a_b == mrd_a_b {
+                                (diag_a_n, mrd_a_n)
+                            } else if diag_b_b == mrd_a_b {
+                                (diag_b_n, mrd_a_n)
+                            } else {
+                                continue;
+                            };
+
+                            let p = chi_square_test_for_proportions(
+                                *a as f64,
+                                diag_pileup_len as f64,
+                                *c as f64,
+                                mrd_pileup_len as f64,
+                            )
+                            .unwrap();
+
+                            if p <= max_p_val && p != 0.0 {
+                                let mut d = diff.lock().unwrap();
+                                // println!(
+                                //     "diff {snp_cols:?} {p} {a} {diag_pileup_len} {c} {mrd_pileup_len}"
+                                // );
+                                *d += 1;
+                            } else {
+                                // println!(
+                                //     "eq {snp_cols:?} {p} {a} {diag_pileup_len} {c} {mrd_pileup_len}"
+                                // );
+                                let mut e = eq.lock().unwrap();
+                                *e += 1;
+                            }
+                        } else {
+                            continue;
+                        }
+                    }
+                }
+            }
+        });
+
+        let diff = Arc::try_unwrap(diff).unwrap().into_inner()?;
+        let eq = Arc::try_unwrap(eq).unwrap().into_inner()?;
+        Ok(diff as f64 * 100.0 / (diff + eq) as f64)
+    }
+}

src/config.rs

@@ -0,0 +1,39 @@
+use std::path::PathBuf;
+
+use serde::{Serialize, Deserialize};
+use anyhow::Result;
+
+#[derive(Serialize, Deserialize, Clone, Debug)]
+pub struct Config {
+    pub longreads_results_dir: String,
+    pub panel_results_dir: String,
+    pub diag_bam_glob: String,
+    pub mrd_bam_glob: String,
+    pub bam_compo_n: usize,
+    pub commun_snp: String,
+    pub max_snp_diff_prop: f64,
+}
+
+impl ::std::default::Default for Config {
+    fn default() -> Self {
+        Self {
+            longreads_results_dir: "/data/longreads_basic_pipe".to_string(),
+            panel_results_dir: "/data/oncoT".to_string(),
+            diag_bam_glob: "/data/longreads_basic_pipe/*/diag/*diag_hs1.bam".to_string(),
+            mrd_bam_glob: "/data/longreads_basic_pipe/*/mrd/*mrd_hs1.bam".to_string(),
+            bam_compo_n: 1000,
+            commun_snp: "/data/ref/hs1/common_snp_T2T.bed.gz".to_string(),
+            max_snp_diff_prop: 0.40,
+        }
+    }
+}
+
+impl Config {
+    pub fn get() -> Result<Self> {
+        Ok(confy::load("pandora_lib_cases", None)?)
+    }
+    pub fn path() -> Result<PathBuf> {
+        Ok(confy::get_configuration_file_path("pandora_lib_cases", None)?)
+    } 
+}
+

src/lib.rs

@@ -0,0 +1,43 @@
+pub mod bam;
+pub mod cases;
+pub mod config;
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use anyhow::{Ok, Result};
+    use indicatif::MultiProgress;
+    use indicatif_log_bridge::LogWrapper;
+
+    #[test]
+    fn it_works() -> Result<()> {
+        let logger =
+            env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("info"))
+                .build();
+        let multi = MultiProgress::new();
+        LogWrapper::new(multi.clone(), logger).try_init().unwrap();
+
+        let cases = cases::Cases::load(multi)?;
+        cases.cases.iter().for_each(|c| println!("{}", c.id));
+
+        Ok(())
+    }
+
+    #[test]
+    fn check_snp() -> Result<()> {
+        let cfg = config::Config::get()?;
+        let name = "LEVASSEUR"; // .43 .55 .51 .46 .55 .47
+        // let name = "CAMARA"; // .12 .15 .24 .22 .21 .24 .13
+        // let name = "HAMROUNE"; // .46 .61 .71 .74 .76 .53 .8 .72
+        let diag_bam = format!("/data/longreads_basic_pipe/{name}/diag/{name}_diag_hs1.bam");
+        let mrd_bam = format!("/data/longreads_basic_pipe/{name}/mrd/{name}_mrd_hs1.bam");
+
+        let diff_snp = cases::DiffSnp::init(&cfg.commun_snp)?;
+        for _ in 0..5 {
+            let diff = diff_snp.diff_prop(&diag_bam, &mrd_bam)?;
+            println!("{diff}");
+        }
+
+        Ok(())
+    }
+}