ok

Cargo.lock

@@ -67,9 +67,9 @@ dependencies = [
 
 [[package]]
 name = "anstyle-query"
-version = "1.0.3"
+version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a64c907d4e79225ac72e2a354c9ce84d50ebb4586dee56c82b3ee73004f537f5"
+checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391"
 dependencies = [
  "windows-sys",
 ]
@@ -184,9 +184,9 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.0.98"
+version = "1.0.99"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "41c270e7540d725e65ac7f1b212ac8ce349719624d7bcff99f8e2e488e8cf03f"
+checksum = "96c51067fd44124faa7f870b4b1c969379ad32b2ba805aa959430ceaa384f695"
 dependencies = [
  "jobserver",
  "libc",
@@ -201,9 +201,9 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
 [[package]]
 name = "clap"
-version = "4.5.4"
+version = "4.5.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "90bc066a67923782aa8515dbaea16946c5bcc5addbd668bb80af688e53e548a0"
+checksum = "5db83dced34638ad474f39f250d7fea9598bdd239eaced1bdf45d597da0f433f"
 dependencies = [
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  "clap_derive",
@@ -211,9 +211,9 @@ dependencies = [
 
 [[package]]
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-version = "4.5.2"
+version = "4.5.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4"
+checksum = "f7e204572485eb3fbf28f871612191521df159bc3e15a9f5064c66dba3a8c05f"
 dependencies = [
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  "anstyle",
@@ -223,21 +223,21 @@ dependencies = [
 
 [[package]]
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-version = "4.5.4"
+version = "4.5.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
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+checksum = "c780290ccf4fb26629baa7a1081e68ced113f1d3ec302fa5948f1c381ebf06c6"
 dependencies = [
  "heck 0.5.0",
  "proc-macro2",
  "quote",
- "syn 2.0.65",
+ "syn 2.0.66",
 ]
 
 [[package]]
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-version = "0.7.0"
+version = "0.7.1"
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+checksum = "4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70"
 
 [[package]]
 name = "cmake"
@@ -459,6 +459,17 @@ dependencies = [
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 ]
 
+[[package]]
+name = "displaydoc"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "487585f4d0c6655fe74905e2504d8ad6908e4db67f744eb140876906c2f3175d"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+]
+
 [[package]]
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@@ -639,14 +650,134 @@ version = "2.1.0"
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 checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4"
 
+[[package]]
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+checksum = "db2fa452206ebee18c4b5c2274dbf1de17008e874b4dc4f0aea9d01ca79e4526"
+dependencies = [
+ "displaydoc",
+ "yoke",
+ "zerofrom",
+ "zerovec",
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+dependencies = [
+ "displaydoc",
+ "litemap",
+ "tinystr",
+ "writeable",
+ "zerovec",
+]
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+dependencies = [
+ "displaydoc",
+ "icu_locid",
+ "icu_locid_transform_data",
+ "icu_provider",
+ "tinystr",
+ "zerovec",
+]
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+dependencies = [
+ "displaydoc",
+ "icu_collections",
+ "icu_normalizer_data",
+ "icu_properties",
+ "icu_provider",
+ "smallvec",
+ "utf16_iter",
+ "utf8_iter",
+ "write16",
+ "zerovec",
+]
+
+[[package]]
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+
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+dependencies = [
+ "displaydoc",
+ "icu_collections",
+ "icu_locid_transform",
+ "icu_properties_data",
+ "icu_provider",
+ "tinystr",
+ "zerovec",
+]
+
+[[package]]
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+
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+checksum = "6ed421c8a8ef78d3e2dbc98a973be2f3770cb42b606e3ab18d6237c4dfde68d9"
+dependencies = [
+ "displaydoc",
+ "icu_locid",
+ "icu_provider_macros",
+ "stable_deref_trait",
+ "tinystr",
+ "writeable",
+ "yoke",
+ "zerofrom",
+ "zerovec",
+]
+
+[[package]]
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+checksum = "1ec89e9337638ecdc08744df490b221a7399bf8d164eb52a665454e60e075ad6"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+]
+
 [[package]]
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+version = "1.0.0"
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-checksum = "634d9b1461af396cad843f47fdba5597a4f9e6ddd4bfb6ff5d85028c25cb12f6"
+checksum = "4716a3a0933a1d01c2f72450e89596eb51dd34ef3c211ccd875acdf1f8fe47ed"
 dependencies = [
- "unicode-bidi",
- "unicode-normalization",
+ "icu_normalizer",
+ "icu_properties",
+ "smallvec",
+ "utf8_iter",
 ]
 
 [[package]]
@@ -843,9 +974,9 @@ dependencies = [
 
 [[package]]
 name = "libz-sys"
-version = "1.1.16"
+version = "1.1.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5e143b5e666b2695d28f6bca6497720813f699c9602dd7f5cac91008b8ada7f9"
+checksum = "c15da26e5af7e25c90b37a2d75cdbf940cf4a55316de9d84c679c9b8bfabf82e"
 dependencies = [
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@@ -860,6 +991,12 @@ version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
 
+[[package]]
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+version = "0.7.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "643cb0b8d4fcc284004d5fd0d67ccf61dfffadb7f75e1e71bc420f4688a3a704"
+
 [[package]]
 name = "lock_api"
 version = "0.4.12"
@@ -899,9 +1036,9 @@ dependencies = [
 
 [[package]]
 name = "memchr"
-version = "2.7.2"
+version = "2.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
+checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "miniz_oxide"
@@ -1137,9 +1274,9 @@ checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
 
 [[package]]
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-version = "300.2.3+3.2.1"
+version = "300.3.1+3.3.1"
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-checksum = "5cff92b6f71555b61bb9315f7c64da3ca43d87531622120fea0195fc761b4843"
+checksum = "7259953d42a81bf137fbbd73bd30a8e1914d6dce43c2b90ed575783a22608b91"
 dependencies = [
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 ]
@@ -1214,7 +1351,7 @@ dependencies = [
 [[package]]
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-source = "git+https://git.t0m4.fr/Thomas/pandora_lib_variants.git#50f254410e8e5e50b1f8203754e9b71381733b33"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_variants.git#00f3f9c2fa5f612d8ef3bb1f6cad0b2cb0ab6fbb"
 dependencies = [
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@@ -1321,9 +1458,9 @@ dependencies = [
 
 [[package]]
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-version = "1.0.83"
+version = "1.0.85"
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-checksum = "0b33eb56c327dec362a9e55b3ad14f9d2f0904fb5a5b03b513ab5465399e9f43"
+checksum = "22244ce15aa966053a896d1accb3a6e68469b97c7f33f284b99f0d576879fc23"
 dependencies = [
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 ]
@@ -1411,9 +1548,9 @@ dependencies = [
 
 [[package]]
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-version = "0.5.1"
+version = "0.5.2"
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-checksum = "469052894dcb553421e483e4209ee581a45100d31b4018de03e5a7ad86374a7e"
+checksum = "c82cf8cff14456045f55ec4241383baeff27af886adb72ffb2162f99911de0fd"
 dependencies = [
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 ]
@@ -1431,9 +1568,9 @@ dependencies = [
 
 [[package]]
 name = "regex"
-version = "1.10.4"
+version = "1.10.5"
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-checksum = "c117dbdfde9c8308975b6a18d71f3f385c89461f7b3fb054288ecf2a2058ba4c"
+checksum = "b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f"
 dependencies = [
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@@ -1443,9 +1580,9 @@ dependencies = [
 
 [[package]]
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+version = "0.4.7"
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-checksum = "86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea"
+checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df"
 dependencies = [
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@@ -1454,9 +1591,9 @@ dependencies = [
 
 [[package]]
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-version = "0.8.3"
+version = "0.8.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adad44e29e4c806119491a7f06f03de4d1af22c3a680dd47f1e6e179439d1f56"
+checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b"
 
 [[package]]
 name = "rusqlite"
@@ -1547,9 +1684,9 @@ checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
 
 [[package]]
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-version = "0.7.1"
+version = "0.7.2"
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-checksum = "f398075ce1e6a179b46f51bd88d0598b92b00d3551f1a2d4ac49e771b56ac354"
+checksum = "c3460605018fdc9612bce72735cba0d27efbcd9904780d44c7e3a9948f96148a"
 dependencies = [
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 ]
@@ -1568,22 +1705,22 @@ checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
 [[package]]
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-version = "1.0.202"
+version = "1.0.203"
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-checksum = "226b61a0d411b2ba5ff6d7f73a476ac4f8bb900373459cd00fab8512828ba395"
+checksum = "7253ab4de971e72fb7be983802300c30b5a7f0c2e56fab8abfc6a214307c0094"
 dependencies = [
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 ]
 
 [[package]]
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-version = "1.0.202"
+version = "1.0.203"
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-checksum = "6048858004bcff69094cd972ed40a32500f153bd3be9f716b2eed2e8217c4838"
+checksum = "500cbc0ebeb6f46627f50f3f5811ccf6bf00643be300b4c3eabc0ef55dc5b5ba"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.65",
+ "syn 2.0.66",
 ]
 
 [[package]]
@@ -1640,9 +1777,9 @@ checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
 
 [[package]]
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-version = "0.16.0"
+version = "0.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2d08e5e1748192713cc281da8b16924fb46be7b0c2431854eadc785823e5696e"
+checksum = "b35a062dbadac17a42e0fc64c27f419b25d6fae98572eb43c8814c9e873d7721"
 dependencies = [
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@@ -1667,7 +1804,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.65",
+ "syn 2.0.66",
 ]
 
 [[package]]
@@ -1683,15 +1820,26 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.65"
+version = "2.0.66"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d2863d96a84c6439701d7a38f9de935ec562c8832cc55d1dde0f513b52fad106"
+checksum = "c42f3f41a2de00b01c0aaad383c5a45241efc8b2d1eda5661812fda5f3cdcff5"
 dependencies = [
  "proc-macro2",
  "quote",
  "unicode-ident",
 ]
 
+[[package]]
+name = "synstructure"
+version = "0.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c8af7666ab7b6390ab78131fb5b0fce11d6b7a6951602017c35fa82800708971"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+]
+
 [[package]]
 name = "term"
 version = "0.7.0"
@@ -1729,24 +1877,19 @@ checksum = "46c3384250002a6d5af4d114f2845d37b57521033f30d5c3f46c4d70e1197533"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.65",
+ "syn 2.0.66",
 ]
 
 [[package]]
-name = "tinyvec"
-version = "1.6.0"
+name = "tinystr"
+version = "0.7.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50"
+checksum = "9117f5d4db391c1cf6927e7bea3db74b9a1c1add8f7eda9ffd5364f40f57b82f"
 dependencies = [
- "tinyvec_macros",
+ "displaydoc",
+ "zerovec",
 ]
 
-[[package]]
-name = "tinyvec_macros"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
-
 [[package]]
 name = "toml"
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@@ -1772,49 +1915,46 @@ version = "1.17.0"
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 checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "08f95100a766bf4f8f28f90d77e0a5461bbdb219042e7679bebe79004fed8d75"
-
 [[package]]
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 checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a56d1686db2308d901306f92a263857ef59ea39678a5458e7cb17f01415101f5"
-dependencies = [
- "tinyvec",
-]
-
 [[package]]
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-version = "0.1.12"
+version = "0.1.13"
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-checksum = "68f5e5f3158ecfd4b8ff6fe086db7c8467a2dfdac97fe420f2b7c4aa97af66d6"
+checksum = "0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d"
 
 [[package]]
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-version = "2.5.0"
+version = "2.5.1"
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-checksum = "31e6302e3bb753d46e83516cae55ae196fc0c309407cf11ab35cc51a4c2a4633"
+checksum = "f7c25da092f0a868cdf09e8674cd3b7ef3a7d92a24253e663a2fb85e2496de56"
 dependencies = [
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  "idna",
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 ]
 
+[[package]]
+name = "utf16_iter"
+version = "1.0.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c8232dd3cdaed5356e0f716d285e4b40b932ac434100fe9b7e0e8e935b9e6246"
+
+[[package]]
+name = "utf8_iter"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6c140620e7ffbb22c2dee59cafe6084a59b5ffc27a8859a5f0d494b5d52b6be"
+
 [[package]]
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-version = "0.2.1"
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 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a"
+checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
 
 [[package]]
 name = "uuid"
@@ -1846,9 +1986,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wide"
-version = "0.7.20"
+version = "0.7.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "21e005a4cc35784183a9e39cb22e9a9c46353ef6a7f113fd8d36ddc58c15ef3c"
+checksum = "8a040b111774ab63a19ef46bbc149398ab372b4ccdcfd719e9814dbd7dfd76c8"
 dependencies = [
  "bytemuck",
  "safe_arch",
@@ -1958,6 +2098,42 @@ version = "0.52.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0"
 
+[[package]]
+name = "write16"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d1890f4022759daae28ed4fe62859b1236caebfc61ede2f63ed4e695f3f6d936"
+
+[[package]]
+name = "writeable"
+version = "0.5.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e9df38ee2d2c3c5948ea468a8406ff0db0b29ae1ffde1bcf20ef305bcc95c51"
+
+[[package]]
+name = "yoke"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6c5b1314b079b0930c31e3af543d8ee1757b1951ae1e1565ec704403a7240ca5"
+dependencies = [
+ "serde",
+ "stable_deref_trait",
+ "yoke-derive",
+ "zerofrom",
+]
+
+[[package]]
+name = "yoke-derive"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "28cc31741b18cb6f1d5ff12f5b7523e3d6eb0852bbbad19d73905511d9849b95"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+ "synstructure",
+]
+
 [[package]]
 name = "zerocopy"
 version = "0.7.34"
@@ -1975,5 +2151,48 @@ checksum = "15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.65",
+ "syn 2.0.66",
+]
+
+[[package]]
+name = "zerofrom"
+version = "0.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "91ec111ce797d0e0784a1116d0ddcdbea84322cd79e5d5ad173daeba4f93ab55"
+dependencies = [
+ "zerofrom-derive",
+]
+
+[[package]]
+name = "zerofrom-derive"
+version = "0.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0ea7b4a3637ea8669cedf0f1fd5c286a17f3de97b8dd5a70a6c167a1730e63a5"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+ "synstructure",
+]
+
+[[package]]
+name = "zerovec"
+version = "0.10.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bb2cc8827d6c0994478a15c53f374f46fbd41bea663d809b14744bc42e6b109c"
+dependencies = [
+ "yoke",
+ "zerofrom",
+ "zerovec-derive",
+]
+
+[[package]]
+name = "zerovec-derive"
+version = "0.10.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "97cf56601ee5052b4417d90c8755c6683473c926039908196cf35d99f893ebe7"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
 ]

src/cases.rs

@@ -68,6 +68,7 @@ impl Cases {
             mrd_bams.insert(case_id, b);
         }
 
+        // Check SNP AF differences between diag and mrd
         let mut cases = Vec::new();
         let diff_snp = DiffSnp::init(&config.commun_snp)?;
         for (id, diag_bam) in diag_bams {
@@ -159,12 +160,26 @@ impl Case {
 
         Ok(())
     }
+
     pub fn n_variants(&self) -> Option<usize> {
         match &self.variants {
             Some(v) => Some(v.len()),
             None => None,
         }
     }
+
+    pub fn variants_stat(&self) -> Option<String> {
+        match &self.variants {
+            Some(v) => {
+                if let std::result::Result::Ok(res) = v.stats() {
+                    Some(res)
+                } else {
+                    None
+                }
+            },
+            None => None,
+        }
+    }
 }
 
 pub struct DiffSnp {

src/lib.rs

@@ -17,7 +17,7 @@ mod tests {
         let multi = MultiProgress::new();
         LogWrapper::new(multi.clone(), logger).try_init().unwrap();
 
-        let cases = cases::Cases::load(multi)?;
+        let cases = cases::Cases::load(multi, None)?;
         cases.cases.iter().for_each(|c| println!("{}\t{:?}", c.id, c.n_variants()));
 
         Ok(())