progresss

Cargo.lock

@@ -31,53 +31,54 @@ dependencies = [
 
 [[package]]
 name = "allocator-api2"
-version = "0.2.16"
+version = "0.2.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5"
+checksum = "5c6cb57a04249c6480766f7f7cef5467412af1490f8d1e243141daddada3264f"
 
 [[package]]
 name = "anstream"
-version = "0.6.13"
+version = "0.6.14"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb"
+checksum = "418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b"
 dependencies = [
  "anstyle",
  "anstyle-parse",
  "anstyle-query",
  "anstyle-wincon",
  "colorchoice",
+ "is_terminal_polyfill",
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle"
-version = "1.0.6"
+version = "1.0.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc"
+checksum = "038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.3"
+version = "0.2.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c"
+checksum = "c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.0.2"
+version = "1.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648"
+checksum = "a64c907d4e79225ac72e2a354c9ce84d50ebb4586dee56c82b3ee73004f537f5"
 dependencies = [
  "windows-sys",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.2"
+version = "3.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7"
+checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19"
 dependencies = [
  "anstyle",
  "windows-sys",
@@ -85,9 +86,9 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.81"
+version = "1.0.83"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0952808a6c2afd1aa8947271f3a60f1a6763c7b912d210184c5149b5cf147247"
+checksum = "25bdb32cbbdce2b519a9cd7df3a678443100e265d5e25ca763b7572a5104f5f3"
 
 [[package]]
 name = "approx"
@@ -100,9 +101,9 @@ dependencies = [
 
 [[package]]
 name = "autocfg"
-version = "1.2.0"
+version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80"
+checksum = "0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0"
 
 [[package]]
 name = "bgzip"
@@ -135,12 +136,6 @@ version = "0.6.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
 
-[[package]]
-name = "bitflags"
-version = "1.3.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
-
 [[package]]
 name = "bitflags"
 version = "2.5.0"
@@ -149,9 +144,9 @@ checksum = "cf4b9d6a944f767f8e5e0db018570623c85f3d925ac718db4e06d0187adb21c1"
 
 [[package]]
 name = "bytemuck"
-version = "1.15.0"
+version = "1.16.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d6d68c57235a3a081186990eca2867354726650f42f7516ca50c28d6281fd15"
+checksum = "78834c15cb5d5efe3452d58b1e8ba890dd62d21907f867f383358198e56ebca5"
 
 [[package]]
 name = "byteorder"
@@ -178,12 +173,13 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.0.90"
+version = "1.0.97"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8cd6604a82acf3039f1144f54b8eb34e91ffba622051189e71b781822d5ee1f5"
+checksum = "099a5357d84c4c61eb35fc8eafa9a79a902c2f76911e5747ced4e032edd8d9b4"
 dependencies = [
  "jobserver",
  "libc",
+ "once_cell",
 ]
 
 [[package]]
@@ -223,7 +219,7 @@ dependencies = [
  "heck 0.5.0",
  "proc-macro2",
  "quote",
- "syn 2.0.57",
+ "syn 2.0.63",
 ]
 
 [[package]]
@@ -243,9 +239,9 @@ dependencies = [
 
 [[package]]
 name = "colorchoice"
-version = "1.0.0"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7"
+checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422"
 
 [[package]]
 name = "confy"
@@ -281,6 +277,19 @@ 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"
@@ -309,6 +318,15 @@ 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"
@@ -432,9 +450,9 @@ dependencies = [
 
 [[package]]
 name = "either"
-version = "1.10.0"
+version = "1.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "11157ac094ffbdde99aa67b23417ebdd801842852b500e395a45a9c0aac03e4a"
+checksum = "a47c1c47d2f5964e29c61246e81db715514cd532db6b5116a25ea3c03d6780a2"
 
 [[package]]
 name = "encode_unicode"
@@ -481,9 +499,9 @@ checksum = "7360491ce676a36bf9bb3c56c1aa791658183a54d2744120f27285738d90465a"
 
 [[package]]
 name = "flate2"
-version = "1.0.28"
+version = "1.0.30"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e"
+checksum = "5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae"
 dependencies = [
  "crc32fast",
  "miniz_oxide",
@@ -509,9 +527,9 @@ dependencies = [
 
 [[package]]
 name = "getrandom"
-version = "0.2.12"
+version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "190092ea657667030ac6a35e305e62fc4dd69fd98ac98631e5d3a2b1575a12b5"
+checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7"
 dependencies = [
  "cfg-if",
  "libc",
@@ -526,9 +544,9 @@ checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
 
 [[package]]
 name = "half"
-version = "2.4.0"
+version = "2.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b5eceaaeec696539ddaf7b333340f1af35a5aa87ae3e4f3ead0532f72affab2e"
+checksum = "6dd08c532ae367adf81c312a4580bc67f1d0fe8bc9c460520283f4c0ff277888"
 dependencies = [
  "cfg-if",
  "crunchy",
@@ -536,9 +554,9 @@ dependencies = [
 
 [[package]]
 name = "hashbrown"
-version = "0.14.3"
+version = "0.14.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604"
+checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
 dependencies = [
  "ahash",
  "allocator-api2",
@@ -575,9 +593,9 @@ checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024"
 
 [[package]]
 name = "hts-sys"
-version = "2.1.1"
+version = "2.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "deebfb779c734d542e7f14c298597914b9b5425e4089aef482eacb5cab941915"
+checksum = "e9f348d14cb4e50444e39fcd6b00302fe2ed2bc88094142f6278391d349a386d"
 dependencies = [
  "bzip2-sys",
  "cc",
@@ -665,6 +683,12 @@ dependencies = [
  "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 = "itoa"
 version = "1.0.11"
@@ -673,9 +697,9 @@ checksum = "49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b"
 
 [[package]]
 name = "jobserver"
-version = "0.1.28"
+version = "0.1.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ab46a6e9526ddef3ae7f787c06f0f2600639ba80ea3eade3d8e670a2230f51d6"
+checksum = "d2b099aaa34a9751c5bf0878add70444e1ed2dd73f347be99003d4577277de6e"
 dependencies = [
  "libc",
 ]
@@ -752,9 +776,9 @@ dependencies = [
 
 [[package]]
 name = "libc"
-version = "0.2.153"
+version = "0.2.154"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
+checksum = "ae743338b92ff9146ce83992f766a31066a91a8c84a45e0e9f21e7cf6de6d346"
 
 [[package]]
 name = "libm"
@@ -768,7 +792,7 @@ version = "0.1.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c0ff37bd590ca25063e35af745c343cb7a0271906fb7b37e4813e8f79f00268d"
 dependencies = [
- "bitflags 2.5.0",
+ "bitflags",
  "libc",
 ]
 
@@ -803,9 +827,9 @@ checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
 
 [[package]]
 name = "lock_api"
-version = "0.4.11"
+version = "0.4.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
+checksum = "07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17"
 dependencies = [
  "autocfg",
  "scopeguard",
@@ -988,7 +1012,7 @@ version = "0.49.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2b94966806ac7aec118d41eea7080bfbd0e8b843ba64f46522c57f0f55cfb1f0"
 dependencies = [
- "bitflags 2.5.0",
+ "bitflags",
  "indexmap",
  "lexical-core",
  "memchr",
@@ -1028,9 +1052,9 @@ dependencies = [
 
 [[package]]
 name = "num-complex"
-version = "0.4.5"
+version = "0.4.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "23c6602fda94a57c990fe0df199a035d83576b496aa29f4e634a8ac6004e68a6"
+checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495"
 dependencies = [
  "num-traits",
 ]
@@ -1046,20 +1070,19 @@ dependencies = [
 
 [[package]]
 name = "num-rational"
-version = "0.4.1"
+version = "0.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0638a1c9d0a3c0914158145bc76cff373a75a627e6ecbfb71cbe6f453a5a19b0"
+checksum = "f83d14da390562dca69fc84082e73e548e1ad308d24accdedd2720017cb37824"
 dependencies = [
- "autocfg",
  "num-integer",
  "num-traits",
 ]
 
 [[package]]
 name = "num-traits"
-version = "0.2.18"
+version = "0.2.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da0df0e5185db44f69b44f26786fe401b6c293d1907744beaa7fa62b2e5a517a"
+checksum = "071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841"
 dependencies = [
  "autocfg",
  "libm",
@@ -1099,6 +1122,15 @@ dependencies = [
  "vcpkg",
 ]
 
+[[package]]
+name = "pandora_lib_report"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_report.git#c4a9a89fae8ee8a4cc2790fe7acee0102e366aa3"
+dependencies = [
+ "crossbeam",
+ "indicatif",
+]
+
 [[package]]
 name = "pandora_lib_variants"
 version = "0.1.0"
@@ -1125,6 +1157,7 @@ dependencies = [
  "noodles-tabix",
  "noodles-vcf",
  "num-integer",
+ "pandora_lib_report",
  "pot",
  "prettytable-rs",
  "rayon",
@@ -1140,22 +1173,22 @@ dependencies = [
 
 [[package]]
 name = "parking_lot_core"
-version = "0.9.9"
+version = "0.9.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e"
+checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
 dependencies = [
  "cfg-if",
  "libc",
  "redox_syscall",
  "smallvec",
- "windows-targets 0.48.5",
+ "windows-targets",
 ]
 
 [[package]]
 name = "paste"
-version = "1.0.14"
+version = "1.0.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "de3145af08024dea9fa9914f381a17b8fc6034dfb00f3a84013f7ff43f29ed4c"
+checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a"
 
 [[package]]
 name = "percent-encoding"
@@ -1208,9 +1241,9 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.79"
+version = "1.0.82"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e835ff2298f5721608eb1a980ecaee1aef2c132bf95ecc026a11b7bf3c01c02e"
+checksum = "8ad3d49ab951a01fbaafe34f2ec74122942fe18a3f9814c3268f1bb72042131b"
 dependencies = [
  "unicode-ident",
 ]
@@ -1223,9 +1256,9 @@ checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
 
 [[package]]
 name = "quote"
-version = "1.0.35"
+version = "1.0.36"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef"
+checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
 dependencies = [
  "proc-macro2",
 ]
@@ -1298,11 +1331,11 @@ dependencies = [
 
 [[package]]
 name = "redox_syscall"
-version = "0.4.1"
+version = "0.5.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
+checksum = "469052894dcb553421e483e4209ee581a45100d31b4018de03e5a7ad86374a7e"
 dependencies = [
- "bitflags 1.3.2",
+ "bitflags",
 ]
 
 [[package]]
@@ -1351,7 +1384,7 @@ version = "0.30.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a78046161564f5e7cd9008aff3b2990b3850dc8e0349119b98e8f251e099f24d"
 dependencies = [
- "bitflags 2.5.0",
+ "bitflags",
  "fallible-iterator",
  "fallible-streaming-iterator",
  "hashlink",
@@ -1400,15 +1433,15 @@ dependencies = [
 
 [[package]]
 name = "rustversion"
-version = "1.0.14"
+version = "1.0.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4"
+checksum = "955d28af4278de8121b7ebeb796b6a45735dc01436d898801014aced2773a3d6"
 
 [[package]]
 name = "ryu"
-version = "1.0.17"
+version = "1.0.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1"
+checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
 
 [[package]]
 name = "safe_arch"
@@ -1433,29 +1466,29 @@ checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
 [[package]]
 name = "serde"
-version = "1.0.197"
+version = "1.0.202"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2"
+checksum = "226b61a0d411b2ba5ff6d7f73a476ac4f8bb900373459cd00fab8512828ba395"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.197"
+version = "1.0.202"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7eb0b34b42edc17f6b7cac84a52a1c5f0e1bb2227e997ca9011ea3dd34e8610b"
+checksum = "6048858004bcff69094cd972ed40a32500f153bd3be9f716b2eed2e8217c4838"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.57",
+ "syn 2.0.63",
 ]
 
 [[package]]
 name = "serde_json"
-version = "1.0.115"
+version = "1.0.117"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "12dc5c46daa8e9fdf4f5e71b6cf9a53f2487da0e86e55808e2d35539666497dd"
+checksum = "455182ea6142b14f93f4bc5320a2b31c1f266b66a4a5c858b013302a5d8cbfc3"
 dependencies = [
  "itoa",
  "ryu",
@@ -1518,9 +1551,9 @@ dependencies = [
 
 [[package]]
 name = "strsim"
-version = "0.11.0"
+version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5ee073c9e4cd00e28217186dbe12796d692868f432bf2e97ee73bed0c56dfa01"
+checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
 [[package]]
 name = "strum_macros"
@@ -1532,7 +1565,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.57",
+ "syn 2.0.63",
 ]
 
 [[package]]
@@ -1548,9 +1581,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.57"
+version = "2.0.63"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "11a6ae1e52eb25aab8f3fb9fca13be982a373b8f1157ca14b897a825ba4a2d35"
+checksum = "bf5be731623ca1a1fb7d8be6f261a3be6d3e2337b8a1f97be944d020c8fcb704"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1579,22 +1612,22 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.58"
+version = "1.0.60"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "03468839009160513471e86a034bb2c5c0e4baae3b43f79ffc55c4a5427b3297"
+checksum = "579e9083ca58dd9dcf91a9923bb9054071b9ebbd800b342194c9feb0ee89fc18"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.58"
+version = "1.0.60"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c61f3ba182994efc43764a46c018c347bc492c79f024e705f46567b418f6d4f7"
+checksum = "e2470041c06ec3ac1ab38d0356a6119054dedaea53e12fbefc0de730a1c08524"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.57",
+ "syn 2.0.63",
 ]
 
 [[package]]
@@ -1660,9 +1693,9 @@ dependencies = [
 
 [[package]]
 name = "unicode-width"
-version = "0.1.11"
+version = "0.1.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e51733f11c9c4f72aa0c160008246859e340b00807569a0da0e7a1079b27ba85"
+checksum = "68f5e5f3158ecfd4b8ff6fe086db7c8467a2dfdac97fe420f2b7c4aa97af66d6"
 
 [[package]]
 name = "url"
@@ -1711,9 +1744,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wide"
-version = "0.7.15"
+version = "0.7.19"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "89beec544f246e679fc25490e3f8e08003bc4bf612068f325120dad4cea02c1c"
+checksum = "aab6594190de06d718a5dbc5fa781ab62f8903797056480e549ca74add6b7065"
 dependencies = [
  "bytemuck",
  "safe_arch",
@@ -1737,11 +1770,11 @@ checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
 
 [[package]]
 name = "winapi-util"
-version = "0.1.6"
+version = "0.1.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596"
+checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
 dependencies = [
- "winapi",
+ "windows-sys",
 ]
 
 [[package]]
@@ -1756,139 +1789,89 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
 dependencies = [
- "windows-targets 0.52.4",
+ "windows-targets",
 ]
 
 [[package]]
 name = "windows-targets"
-version = "0.48.5"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
+checksum = "6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb"
 dependencies = [
- "windows_aarch64_gnullvm 0.48.5",
- "windows_aarch64_msvc 0.48.5",
- "windows_i686_gnu 0.48.5",
- "windows_i686_msvc 0.48.5",
- "windows_x86_64_gnu 0.48.5",
- "windows_x86_64_gnullvm 0.48.5",
- "windows_x86_64_msvc 0.48.5",
+ "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-targets"
-version = "0.52.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7dd37b7e5ab9018759f893a1952c9420d060016fc19a472b4bb20d1bdd694d1b"
-dependencies = [
- "windows_aarch64_gnullvm 0.52.4",
- "windows_aarch64_msvc 0.52.4",
- "windows_i686_gnu 0.52.4",
- "windows_i686_msvc 0.52.4",
- "windows_x86_64_gnu 0.52.4",
- "windows_x86_64_gnullvm 0.52.4",
- "windows_x86_64_msvc 0.52.4",
-]
-
-[[package]]
-name = "windows_aarch64_gnullvm"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
-
 [[package]]
 name = "windows_aarch64_gnullvm"
-version = "0.52.4"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bcf46cf4c365c6f2d1cc93ce535f2c8b244591df96ceee75d8e83deb70a9cac9"
+checksum = "7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263"
 
 [[package]]
 name = "windows_aarch64_msvc"
-version = "0.48.5"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
-
-[[package]]
-name = "windows_aarch64_msvc"
-version = "0.52.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da9f259dd3bcf6990b55bffd094c4f7235817ba4ceebde8e6d11cd0c5633b675"
+checksum = "9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6"
 
 [[package]]
 name = "windows_i686_gnu"
-version = "0.48.5"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
+checksum = "88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670"
 
 [[package]]
-name = "windows_i686_gnu"
-version = "0.52.4"
+name = "windows_i686_gnullvm"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3"
+checksum = "87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9"
 
 [[package]]
 name = "windows_i686_msvc"
-version = "0.48.5"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
-
-[[package]]
-name = "windows_i686_msvc"
-version = "0.52.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02"
+checksum = "db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf"
 
 [[package]]
 name = "windows_x86_64_gnu"
-version = "0.48.5"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
-
-[[package]]
-name = "windows_x86_64_gnu"
-version = "0.52.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03"
-
-[[package]]
-name = "windows_x86_64_gnullvm"
-version = "0.48.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
+checksum = "4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9"
 
 [[package]]
 name = "windows_x86_64_gnullvm"
-version = "0.52.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177"
-
-[[package]]
-name = "windows_x86_64_msvc"
-version = "0.48.5"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
+checksum = "852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596"
 
 [[package]]
 name = "windows_x86_64_msvc"
-version = "0.52.4"
+version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8"
+checksum = "bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0"
 
 [[package]]
 name = "zerocopy"
-version = "0.7.32"
+version = "0.7.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be"
+checksum = "ae87e3fcd617500e5d106f0380cf7b77f3c6092aae37191433159dda23cfb087"
 dependencies = [
  "zerocopy-derive",
 ]
 
 [[package]]
 name = "zerocopy-derive"
-version = "0.7.32"
+version = "0.7.34"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6"
+checksum = "15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.57",
+ "syn 2.0.63",
 ]

Cargo.toml

@@ -41,3 +41,5 @@ dashmap = { version = "5.5.3", features = ["rayon", "serde"] }
 crossbeam-deque = "0.8.5"
 trc = "1.2.4"
 pot = "=3.0.0"
+pandora_lib_report = { git = "https://git.t0m4.fr/Thomas/pandora_lib_report.git" }
+

src/variants.rs

@@ -30,15 +30,15 @@ use anyhow::{anyhow, Context, Ok, Result};
 use csv::ReaderBuilder;
 use dashmap::DashMap;
 use hashbrown::HashMap;
-use indicatif::{MultiProgress, ParallelProgressIterator};
+use indicatif::{MultiProgress, ParallelProgressIterator, ProgressBar};
 use log::{info, warn};
 use noodles_core::{region::Region, Position};
 use noodles_fasta::indexed_reader::Builder as FastaBuilder;
 use noodles_gff as gff;
 
+use pandora_lib_report::Reporter;
 use rayon::prelude::*;
 use serde::{Deserialize, Serialize};
-use std::io::Write;
 use std::{
     env::temp_dir,
     fmt,
@@ -49,6 +49,7 @@ use std::{
         Arc,
     },
 };
+use std::{io::Write, path::Path};
 
 // chr12:25116542|G>T KRAS
 #[derive(Debug, Clone)]
@@ -59,7 +60,7 @@ pub struct Variants {
     pub stats_vcf: StatsVCF,
     pub stats_bam: StatsBAM,
     pub cfg: Config,
-    pub mp: MultiProgress,
+    pub reporter: Reporter,
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize, Default)]
@@ -108,7 +109,7 @@ impl fmt::Display for StatsBAM {
 }
 
 impl Variants {
-    pub fn from_vec(name: String, mp: &MultiProgress, data: Vec<Variant>) -> Self {
+    pub fn from_vec(name: String, reporter: Reporter, data: Vec<Variant>) -> Self {
         Self {
             name,
             data,
@@ -116,7 +117,7 @@ impl Variants {
             stats_vcf: StatsVCF::default(),
             stats_bam: StatsBAM::default(),
             cfg: Config::get().unwrap(),
-            mp: mp.clone(),
+            reporter,
         }
     }
 
@@ -124,16 +125,19 @@ impl Variants {
         name: String,
         v: Vec<(&str, &VCFSource, &VariantType)>,
         cfg: &Config,
-        mp: MultiProgress,
+        reporter: Reporter,
     ) -> Result<Self> {
-        let pg = mp.add(new_pg(v.len() as u64));
-        pg.set_message("Reading VCF");
+        let reporter_msg = "Reading VCF".to_string();
+        if reporter.with_multi_progress {
+            reporter.create_counter(&reporter_msg, Some(v.len() as u64));
+        } else {
+            reporter.create_counter(&reporter_msg, None);
+        }
 
         let constit: Arc<DashMap<String, Variant>> = Arc::new(DashMap::new());
         let n_constit = AtomicI32::new(0);
         let data: Vec<Variant> = v
             .par_iter()
-            // .progress_count(v.len() as u64)
             .flat_map(|(path, source, variant_type)| {
                 let r = match variant_type {
                     VariantType::Somatic => read_vcf(path, source, variant_type).unwrap(),
@@ -154,7 +158,7 @@ impl Variants {
                         vec![]
                     }
                 };
-                pg.inc(1);
+                reporter.inc(&reporter_msg);
                 r
             })
             .collect();
@@ -163,9 +167,10 @@ impl Variants {
         let stats_bam = StatsBAM::default();
 
         let constit = Arc::try_unwrap(constit).unwrap();
-        let elapsed = pg.elapsed();
-        pg.finish();
+
+        let (val, elapsed) = reporter.finish(&reporter_msg)?;
         info!("{} variants parsed from somatic VCFs and {} variants positions parsed from constitutionnal VCFs. Executed in {}s", data.len(), constit.len(), elapsed.as_secs());
+
         let cfg = cfg.clone();
 
         return Ok(Self {
@@ -175,14 +180,20 @@ impl Variants {
             stats_vcf,
             stats_bam,
             cfg,
-            mp: mp.clone(),
+            reporter,
         });
     }
 
     pub fn vcf_filters(&mut self) {
         let cfg = &self.cfg;
-        let pg = self.mp.add(new_pg_speed(self.data.len() as u64));
-        pg.set_message("VCF filtering");
+
+        let reporter_msg = "Filtering variations with VCF data".to_string();
+        if self.reporter.with_multi_progress {
+            self.reporter
+                .create_counter(&reporter_msg, Some(self.data.len() as u64));
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
 
         let n_tumoral_init = self.len();
         let n_constit_init = self.constit_len();
@@ -261,7 +272,7 @@ impl Variants {
                         }
                     }
                 }
-                pg.inc(1);
+                self.reporter.inc(&reporter_msg);
                 tumoral
             })
             .collect();
@@ -277,18 +288,22 @@ impl Variants {
             n_loh,
             n_low_mrd_depth,
         };
-        // let elapsed = start.elapsed();
-        let elapsed = pg.elapsed();
-        pg.finish();
-        info!("{}. Executed in {}s", self.stats_vcf, elapsed.as_secs());
+
+        let (_, d) = self.reporter.finish(&reporter_msg).unwrap();
+        info!("{}. Executed in {}s", self.stats_vcf, d.as_secs());
     }
 
     /// Filter variants by reading informations from constist BAM.
     pub fn bam_filters(&mut self, mrd_bam: &str) {
         let cfg = &self.cfg;
-        // let start = Instant::now();
-        let pg = self.mp.add(new_pg_speed(self.data.len() as u64));
-        pg.set_message("BAM filtering");
+
+        let reporter_msg = "Filtering variations with BAM data".to_string();
+        if self.reporter.with_multi_progress {
+            self.reporter
+                .create_counter(&reporter_msg, Some(self.data.len() as u64));
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
 
         let min_mrd_depth = cfg.min_mrd_depth;
         info!("Filtering Constitutionnal (Alt base found in BAM pileup), LowDiversity (sequence +/- 20nt around variant with entropy < {}), LowMRDDepth (BAM pileup depth < {}) variants by BAM pileup fetching of {} likely somatic variants", cfg.min_diversity, min_mrd_depth, self.stats_vcf.n_tumoral_init - (self.stats_vcf.n_constit + self.stats_vcf.n_loh + self.stats_vcf.n_low_mrd_depth) as usize);
@@ -307,7 +322,7 @@ impl Variants {
                 .unwrap();
 
             for tumoral in chunk.iter_mut() {
-                pg.inc(1);
+                self.reporter.inc(&reporter_msg);
 
                 if tumoral.annotations.len() > 0 {
                     n_already.fetch_add(1, Ordering::SeqCst);
@@ -423,18 +438,27 @@ impl Variants {
             n_low_diversity,
             n_somatic,
         };
-        let elapsed = pg.elapsed();
-        pg.finish();
-        info!("{}. Executed in {}s", self.stats_vcf, elapsed.as_secs());
+        let (_, d) = self.reporter.finish(&reporter_msg).unwrap();
+        info!("{}. Executed in {}s", self.stats_bam, d.as_secs());
     }
 
+    /// Retrieve variants annotated with VariantCategory
     pub fn get_cat(&mut self, cat: &VariantCategory) -> Vec<Variant> {
-        let pg = self.mp.add(new_pg_speed(self.data.len() as u64));
-        pg.set_message(format!("Get cat {:?}", cat));
-        self.data
+        let reporter_msg = format!("Filtering category {cat:?}");
+        info!("{reporter_msg}");
+        if self.reporter.with_multi_progress {
+            self.reporter
+                .create_counter(&reporter_msg, Some(self.data.len() as u64));
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
+
+        let data = self
+            .data
             .par_iter()
-            .progress_with(pg)
             .flat_map(|e| {
+                self.reporter.inc(&reporter_msg);
+
                 if e.annotations
                     .iter()
                     .filter(|e| match e {
@@ -449,36 +473,67 @@ impl Variants {
                     vec![]
                 }
             })
-            .collect::<Vec<Variant>>()
+            .collect::<Vec<Variant>>();
+        let (_, d) = self.reporter.finish(&reporter_msg).unwrap();
+        info!(
+            "{} variants annotated with category {cat:?} retrieved. Executed in {}s",
+            data.len(),
+            d.as_secs()
+        );
+        data
     }
 
+    /// Write VCF of variants annotated with the specified the category.
     pub fn write_vcf_cat(&mut self, path: &str, cat: &VariantCategory) -> Result<()> {
-        info!("Writing VCF {}", path);
-
         let mut to_write = sort_variants(self.get_cat(cat), &self.cfg.dict_file)?;
-        let pg = self.mp.add(new_pg_speed(to_write.len() as u64));
-        pg.set_message("Writing VCF");
+
+        let reporter_msg = format!(
+            "Writing VCF {}",
+            Path::new(path).file_name().unwrap().to_str().unwrap()
+        );
+        info!("{reporter_msg}");
+        if self.reporter.with_multi_progress {
+            self.reporter
+                .create_counter(&reporter_msg, Some(to_write.len() as u64));
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
 
         let mut w = VariantWritter::new(path, &self.cfg.dict_file)?;
         for row in to_write.iter_mut() {
             w.write_variant(row)?;
-            pg.inc(1);
+            self.reporter.inc(&reporter_msg);
         }
         w.write_index_finish()?;
+        let (n, d) = self.reporter.finish(&reporter_msg)?;
+        info!(
+            "{} variants with category {cat:?} written. Executed in {}s",
+            n,
+            d.as_secs()
+        );
+
         Ok(())
     }
 
-    /// Keep variants annotated Somatic
+    /// Keep variants annotated Somatic and Variants without annotation.
     pub fn keep_somatics_un(&mut self) {
-        let pg = self.mp.add(new_pg_speed(self.data.len() as u64));
-        pg.set_message("Filtering Variants");
+        let reporter_msg = "Keeping somatic variants".to_string();
+        info!("{reporter_msg}");
+        if self.reporter.with_multi_progress {
+            self.reporter
+                .create_counter(&reporter_msg, Some(self.data.len() as u64));
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
 
+        let mut filtered_out = 0u64;
+        let mut keeped = 0u64;
         self.data = self
             .data
             .par_iter_mut()
-            .progress_with(pg)
             .flat_map(|e| {
-                // keep unannotated and somatic
+                self.reporter.inc(&reporter_msg);
+                // Keep un annotated and somatic
                 if e.annotations
                     .iter()
                     .filter(|a| match a {
@@ -491,23 +546,42 @@ impl Variants {
                     .count()
                     == 0
                 {
+                    keeped += 1;
                     vec![e]
                 } else {
+                    filtered_out += 1;
                     vec![]
                 }
             })
             .map(|e| e.clone())
             .collect();
+
+        let (_, d) = self.reporter.finish(&reporter_msg).unwrap();
+        info!(
+            "{keeped} variants conserved and {filtered_out} filtered out. Executed in {}s",
+            d.as_secs()
+        );
     }
 
-    /// Annotate with VEP
+    /// Annotate with VEP.
     pub fn vep(&mut self) {
-        let pg = self.mp.add(new_pg_speed(self.len() as u64));
-        pg.set_message("VEP");
+        let reporter_msg = "VEP annotation".to_string();
+        info!("{reporter_msg}");
+        if self.reporter.with_multi_progress {
+            self.reporter.create_counter(
+                &reporter_msg,
+                Some((self.len() as f64 / self.cfg.vep_chunk_size as f64) as u64),
+            );
+        } else {
+            self.reporter.create_counter(&reporter_msg, None);
+        }
+
         self.data
             .par_chunks_mut(self.cfg.vep_chunk_size)
-            .progress_with(pg)
-            .for_each(|chunks| vep_chunk(chunks).unwrap());
+            .for_each(|chunks| {
+                vep_chunk(chunks).unwrap();
+                self.reporter.inc(&reporter_msg);
+            });
     }
 
     /// sort_variants TODO
@@ -517,7 +591,7 @@ impl Variants {
         Ok(())
     }
 
-    /// 
+    ///
     pub fn merge(&mut self) {
         let pg = self.mp.add(new_pg_speed(self.len() as u64));
         pg.set_message("Merging Variants by contig, positions, ref, alt");