full

Cargo.lock

@@ -538,6 +538,17 @@ version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
 
+[[package]]
+name = "average"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3a237a6822e1c3c98e700b6db5b293eb341b7524dcb8d227941245702b7431dc"
+dependencies = [
+ "easy-cast",
+ "float-ord",
+ "num-traits",
+]
+
 [[package]]
 name = "base64"
 version = "0.21.7"
@@ -550,29 +561,99 @@ version = "0.22.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
 
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a00dc851838a2120612785d195287475a3ac45514741da670b735818822129a0"
+dependencies = [
+ "bitflags 2.6.0",
+ "cexpr",
+ "clang-sys",
+ "itertools",
+ "lazy_static",
+ "lazycell",
+ "proc-macro2",
+ "quote",
+ "regex",
+ "rustc-hash",
+ "shlex",
+ "syn 2.0.71",
+]
+
+[[package]]
+name = "bio-types"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1cc7edd677651969cc262a8dfb870f0c2266c3ceeaf863d742982e39699ff460"
+dependencies = [
+ "derive-new 0.6.0",
+ "lazy_static",
+ "regex",
+ "strum_macros",
+ "thiserror",
+]
+
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+[[package]]
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+checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
+
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+
 [[package]]
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 checksum = "514de17de45fdb8dc022b1a7975556c53c86f9f0aa5f534b98977b171857c2c9"
 
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc"
+dependencies = [
+ "cc",
+ "libc",
+ "pkg-config",
+]
+
 [[package]]
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 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "907d8581360765417f8f2e0e7d602733bbed60156b4465b7617243689ef9b83d"
+dependencies = [
+ "jobserver",
+ "libc",
+ "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"
@@ -594,6 +675,26 @@ dependencies = [
  "windows-targets",
 ]
 
+[[package]]
+name = "clang-sys"
+version = "1.8.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b023947811758c97c59bf9d1c188fd619ad4718dcaa767947df1cadb14f39f4"
+dependencies = [
+ "glob",
+ "libc",
+ "libloading",
+]
+
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130"
+dependencies = [
+ "cc",
+]
+
 [[package]]
 name = "colorchoice"
 version = "1.0.1"
@@ -626,6 +727,31 @@ version = "0.8.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f"
 
+[[package]]
+name = "crossbeam-deque"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d"
+dependencies = [
+ "crossbeam-epoch",
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-epoch"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e"
+dependencies = [
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-utils"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80"
+
 [[package]]
 name = "crunchy"
 version = "0.2.2"
@@ -653,6 +779,64 @@ dependencies = [
  "memchr",
 ]
 
+[[package]]
+name = "curl-sys"
+version = "0.4.73+curl-8.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "450ab250ecf17227c39afb9a2dd9261dc0035cb80f2612472fc0c4aac2dcb84d"
+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"
+
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 1.0.109",
+]
+
+[[package]]
+name = "derive-new"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.71",
+]
+
+[[package]]
+name = "easy-cast"
+version = "0.5.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "10936778145f3bea71fd9bf61332cce28c28e96a380714f7ab34838b80733fd6"
+dependencies = [
+ "libm",
+]
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0"
+
 [[package]]
 name = "env_filter"
 version = "0.1.0"
@@ -688,8 +872,8 @@ version = "23.5.26"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4dac53e22462d78c16d64a1cd22371b54cc3fe94aa15e7886a2fa6e5d1ab8640"
 dependencies = [
- "bitflags",
- "rustc_version",
+ "bitflags 1.3.2",
+ "rustc_version 0.4.0",
 ]
 
 [[package]]
@@ -698,8 +882,32 @@ version = "24.3.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "8add37afff2d4ffa83bc748a70b4b1370984f6980768554182424ef71447c35f"
 dependencies = [
- "bitflags",
- "rustc_version",
+ "bitflags 1.3.2",
+ "rustc_version 0.4.0",
+]
+
+[[package]]
+name = "float-ord"
+version = "0.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8ce81f49ae8a0482e4c55ea62ebbd7e5a686af544c00b9d090bba3ff9be97b3d"
+
+[[package]]
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+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]]
@@ -736,6 +944,29 @@ version = "0.14.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
 
+[[package]]
+name = "heck"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e9f348d14cb4e50444e39fcd6b00302fe2ed2bc88094142f6278391d349a386d"
+dependencies = [
+ "bindgen",
+ "bzip2-sys",
+ "cc",
+ "curl-sys",
+ "fs-utils",
+ "glob",
+ "libz-sys",
+ "lzma-sys",
+ "openssl-sys",
+]
+
 [[package]]
 name = "humantime"
 version = "2.1.0"
@@ -765,6 +996,22 @@ dependencies = [
  "cc",
 ]
 
+[[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]]
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+version = "0.2.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c"
+
 [[package]]
 name = "indexmap"
 version = "2.2.6"
@@ -781,12 +1028,30 @@ 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 = "js-sys"
 version = "0.3.69"
@@ -802,6 +1067,12 @@ version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
+[[package]]
+name = "lazycell"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55"
+
 [[package]]
 name = "lexical-core"
 version = "0.8.5"
@@ -872,24 +1143,89 @@ version = "0.2.155"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c"
 
+[[package]]
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+checksum = "e310b3a6b5907f99202fcdb4960ff45b93735d7c7d96b760fcff8db2dc0e103d"
+dependencies = [
+ "cfg-if",
+ "windows-targets",
+]
+
 [[package]]
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 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058"
 
+[[package]]
+name = "libz-sys"
+version = "1.1.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c15da26e5af7e25c90b37a2d75cdbf940cf4a55316de9d84c679c9b8bfabf82e"
+dependencies = [
+ "cc",
+ "cmake",
+ "libc",
+ "pkg-config",
+ "vcpkg",
+]
+
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
+
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 checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
 
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5fda04ab3764e6cde78b9974eec4f779acaba7c4e84b36eca3cf77c581b85d27"
+dependencies = [
+ "cc",
+ "libc",
+ "pkg-config",
+]
+
 [[package]]
 name = "memchr"
 version = "2.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
+[[package]]
+name = "minimal-lexical"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
+
+[[package]]
+name = "newtype_derive"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec"
+dependencies = [
+ "rustc_version 0.1.7",
+]
+
+[[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"
 version = "0.4.3"
@@ -970,6 +1306,41 @@ version = "1.19.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
 
+[[package]]
+name = "openssl-src"
+version = "300.3.1+3.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7259953d42a81bf137fbbd73bd30a8e1914d6dce43c2b90ed575783a22608b91"
+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_pileup"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_pileup.git#869e07f8d4dca9174b318d131799386a9576cf98"
+dependencies = [
+ "anyhow",
+ "average",
+ "env_logger",
+ "log",
+ "rayon",
+ "rust-htslib",
+]
+
 [[package]]
 name = "pandora_lib_pod5"
 version = "0.1.0"
@@ -990,11 +1361,24 @@ dependencies = [
  "env_logger",
  "glob",
  "log",
+ "pandora_lib_pileup",
  "pandora_lib_pod5",
  "regex",
  "serde",
 ]
 
+[[package]]
+name = "percent-encoding"
+version = "2.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e"
+
+[[package]]
+name = "pkg-config"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d231b230927b5e4ad203db57bbcbee2802f6bce620b1e4a9024a07d94e2907ec"
+
 [[package]]
 name = "podders"
 version = "0.1.4"
@@ -1016,6 +1400,12 @@ 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"
@@ -1025,6 +1415,26 @@ dependencies = [
  "proc-macro2",
 ]
 
+[[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 = "regex"
 version = "1.10.5"
@@ -1054,21 +1464,70 @@ version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b"
 
+[[package]]
+name = "rust-htslib"
+version = "0.47.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "41f1796800e73ebb282c6fc5c03f1fe160e867e01114a58a7e115ee3c1d02482"
+dependencies = [
+ "bio-types",
+ "byteorder",
+ "custom_derive",
+ "derive-new 0.5.9",
+ "hts-sys",
+ "ieee754",
+ "lazy_static",
+ "libc",
+ "libz-sys",
+ "linear-map",
+ "newtype_derive",
+ "regex",
+ "thiserror",
+ "url",
+]
+
+[[package]]
+name = "rustc-hash"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2"
+
+[[package]]
+name = "rustc_version"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084"
+dependencies = [
+ "semver 0.1.20",
+]
+
 [[package]]
 name = "rustc_version"
 version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366"
 dependencies = [
- "semver",
+ "semver 1.0.23",
 ]
 
+[[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 = "semver"
+version = "0.1.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
+
 [[package]]
 name = "semver"
 version = "1.0.23"
@@ -1092,7 +1551,7 @@ checksum = "e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.71",
 ]
 
 [[package]]
@@ -1106,12 +1565,42 @@ dependencies = [
  "serde",
 ]
 
+[[package]]
+name = "shlex"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
+
 [[package]]
 name = "static_assertions"
 version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
 
+[[package]]
+name = "strum_macros"
+version = "0.26.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4c6bee85a5a24955dc440386795aa378cd9cf82acd5f764469152d2270e581be"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "quote",
+ "rustversion",
+ "syn 2.0.71",
+]
+
+[[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 = "2.0.71"
@@ -1123,6 +1612,26 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "thiserror"
+version = "1.0.62"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f2675633b1499176c2dff06b0856a27976a8f9d436737b4cf4f312d4d91d8bbb"
+dependencies = [
+ "thiserror-impl",
+]
+
+[[package]]
+name = "thiserror-impl"
+version = "1.0.62"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d20468752b09f49e909e55a5d338caa8bedf615594e9d80bc4c565d30faf798c"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.71",
+]
+
 [[package]]
 name = "tiny-keccak"
 version = "2.0.2"
@@ -1132,12 +1641,53 @@ dependencies = [
  "crunchy",
 ]
 
+[[package]]
+name = "tinyvec"
+version = "1.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "445e881f4f6d382d5f27c034e25eb92edd7c784ceab92a0937db7f2e9471b938"
+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 = "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 = "url"
+version = "2.5.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "22784dbdf76fdde8af1aeda5622b546b422b6fc585325248a2bf9f5e41e94d6c"
+dependencies = [
+ "form_urlencoded",
+ "idna",
+ "percent-encoding",
+]
+
 [[package]]
 name = "utf8parse"
 version = "0.2.2"
@@ -1153,6 +1703,12 @@ dependencies = [
  "getrandom",
 ]
 
+[[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"
@@ -1186,7 +1742,7 @@ dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.71",
  "wasm-bindgen-shared",
 ]
 
@@ -1208,7 +1764,7 @@ checksum = "e94f17b526d0a461a191c78ea52bbce64071ed5c04c9ffe424dcb38f74171bb7"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.71",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
@@ -1318,5 +1874,5 @@ checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn",
+ "syn 2.0.71",
 ]

Cargo.toml

@@ -9,6 +9,7 @@ env_logger = "^0.11.3"
 anyhow = "1.0.86"
 glob = "0.3.1"
 pandora_lib_pod5 = { git = "https://git.t0m4.fr/Thomas/pandora_lib_pod5.git" }
+pandora_lib_pileup = { git = "https://git.t0m4.fr/Thomas/pandora_lib_pileup.git" }
 regex = "1.10.5"
 chrono = "0.4.38"
 csv = "1.3.0"

src/lib.rs

@@ -30,8 +30,8 @@ mod tests {
         let _ = env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("info"))
             .build();
 
-        let runs = Runs::import_dir("/data/store/banana-pool/run_data", "/data/flow_cells.tsv")?;
-        runs.print_info();
+        let runs = Runs::import_dir("/home/prom/store/banana-pool/run_data", "/data/flow_cells.tsv")?;
+        runs.check_local("/data/longreads_basic_pipe")?;
         Ok(())
     }
 }

src/pod5.rs

@@ -11,6 +11,7 @@ use std::{
     fs::{self, File, Metadata},
     os::unix::fs::MetadataExt,
     path::PathBuf,
+    str::FromStr,
     usize,
 };
 
@@ -265,6 +266,65 @@ impl Runs {
             });
         });
     }
+
+    pub fn check_local(&self, dir: &str) -> anyhow::Result<()> {
+        let mut res = Vec::new();
+        for run in self.runs.iter() {
+            for fc in run.flowcells.iter() {
+                for c in fc.cases.iter() {
+                    let bases_called = if let std::result::Result::Ok(p) =
+                        PathBuf::from_str(&format!(
+                            "{dir}/{}/{}/{}_{}_hs1.bam",
+                            c.id,
+                            c.time_point.to_lowercase(),
+                            c.id,
+                            c.time_point.to_lowercase()
+                        )) {
+                        if p.exists() {
+                            let has_id = pandora_lib_pileup::bam_compo(p.to_str().unwrap(), 20000).unwrap()
+                                .iter()
+                                .flat_map(|(rg, _)| {
+                                    if let Some(index) = rg.find('_') {
+                                        let fc_id: &str = &rg[..index];
+                                        vec![fc_id.to_string()]
+                                    } else {
+                                        vec![]
+                                    }
+                                })
+                                .filter(|i| *i == fc.pod5_info.acquisition_id)
+                                .count()
+                            > 0;
+                            if has_id {
+                                "✅".to_string()
+                            } else {
+                                "❌".to_string()
+                            }
+                        } else {
+                            "❌".to_string()
+                        }
+                    } else {
+                        "❌".to_string()
+                    };
+
+                    let s = [
+                        c.id.to_string(),
+                        c.time_point.to_string(),
+                        c.barcode.to_string(),
+                        run.run_name.clone(),
+                        fc.flowcell_name.to_string(),
+                        fc.pod5_type.to_string(),
+                        fc.pod5_info.acquisition_id.clone(),
+                        bases_called,
+                    ]
+                    .join("\t");
+                    res.push(s);
+                }
+            }
+        }
+        res.sort();
+        println!("{}", res.join("\n"));
+        Ok(())
+    }
 }
 
 #[derive(Debug, Deserialize, Clone)]