up

Cargo.lock

@@ -1,6 +1,6 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 3
+version = 4
 
 [[package]]
 name = "addr2line"
@@ -144,6 +144,15 @@ dependencies = [
  "simd-abstraction",
 ]
 
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad"
+dependencies = [
+ "serde",
+]
+
 [[package]]
 name = "bindgen"
 version = "0.69.4"
@@ -156,12 +165,15 @@ dependencies = [
  "itertools",
  "lazy_static",
  "lazycell",
+ "log",
+ "prettyplease",
  "proc-macro2",
  "quote",
  "regex",
  "rustc-hash",
  "shlex",
- "syn 2.0.77",
+ "syn",
+ "which 4.4.2",
 ]
 
 [[package]]
@@ -174,9 +186,24 @@ dependencies = [
  "lazy_static",
  "regex",
  "strum_macros 0.26.4",
- "thiserror",
+ "thiserror 1.0.63",
+]
+
+[[package]]
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+version = "0.5.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1"
+dependencies = [
+ "bit-vec",
 ]
 
+[[package]]
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+version = "0.6.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
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+
 [[package]]
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 version = "0.10.2"
@@ -195,6 +222,18 @@ version = "2.6.0"
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 checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
 
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1bc2832c24239b0141d5674bb9174f9d68a8b5b3f2753311927c172ca46f7e9c"
+dependencies = [
+ "funty",
+ "radium",
+ "tap",
+ "wyz",
+]
+
 [[package]]
 name = "block-buffer"
 version = "0.10.4"
@@ -261,9 +300,9 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
 [[package]]
 name = "charming"
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 dependencies = [
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  "handlebars",
@@ -320,10 +359,10 @@ dependencies = [
 ]
 
 [[package]]
-name = "convert_case"
-version = "0.4.0"
+name = "cooked-waker"
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+checksum = "147be55d677052dabc6b22252d5dd0fd4c29c8c27aa4f2fbef0f94aa003b406f"
 
 [[package]]
 name = "cpufeatures"
@@ -407,9 +446,9 @@ dependencies = [
 
 [[package]]
 name = "curl-sys"
-version = "0.4.75+curl-8.10.0"
+version = "0.4.78+curl-8.11.0"
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+checksum = "8eec768341c5c7789611ae51cf6c459099f22e64a5d5d0ce4892434e33821eaf"
 dependencies = [
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  "libc",
@@ -465,65 +504,68 @@ dependencies = [
 
 [[package]]
 name = "deno_core"
-version = "0.232.0"
+version = "0.311.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "229ffd108e028b148a1a5a6122f771bc7c37094170226f44b8b93b3a9b79d114"
+checksum = "5e09bd55da542fa1fde753aff617c355b5d782e763ab2a19e4371a56d7844cac"
 dependencies = [
  "anyhow",
+ "bincode",
+ "bit-set",
+ "bit-vec",
  "bytes",
+ "cooked-waker",
+ "deno_core_icudata",
  "deno_ops",
  "deno_unsync",
  "futures",
  "libc",
- "log",
+ "memoffset",
  "parking_lot",
+ "percent-encoding",
  "pin-project",
  "serde",
  "serde_json",
  "serde_v8",
  "smallvec",
  "sourcemap",
+ "static_assertions",
  "tokio",
  "url",
  "v8",
 ]
 
+[[package]]
+name = "deno_core_icudata"
+version = "0.0.73"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a13951ea98c0a4c372f162d669193b4c9d991512de9f2381dd161027f34b26b1"
+
 [[package]]
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+version = "0.187.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f7dde627916f8539f3f0d2e754dda40810c8ca4d655f2eaac1ef54785a12fd27"
+checksum = "e040fd4def8a67538fe38c9955fd970efc9f44284bd69d44f8992a456afd665d"
 dependencies = [
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  "proc-macro2",
  "quote",
  "strum",
  "strum_macros 0.25.3",
- "syn 2.0.77",
- "thiserror",
+ "syn",
+ "thiserror 1.0.63",
 ]
 
 [[package]]
 name = "deno_unsync"
-version = "0.3.10"
+version = "0.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c3c8b95582c2023dbb66fccc37421b374026f5915fa507d437cb566904db9a3a"
+checksum = "d774fd83f26b24f0805a6ab8b26834a0d06ceac0db517b769b1e4633c96a2057"
 dependencies = [
+ "futures",
  "parking_lot",
  "tokio",
 ]
 
-[[package]]
-name = "derive-new"
-version = "0.5.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
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-dependencies = [
- "proc-macro2",
- "quote",
- "syn 1.0.109",
-]
-
 [[package]]
 name = "derive-new"
 version = "0.6.0"
@@ -532,20 +574,18 @@ checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
-name = "derive_more"
-version = "0.99.18"
+name = "derive-new"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5f33878137e4dafd7fa914ad4e259e18a4e8e532b9617a2d0150262bf53abfce"
+checksum = "2cdc8d50f426189eef89dac62fabfa0abb27d5cc008f25bf4156a0203325becc"
 dependencies = [
- "convert_case",
  "proc-macro2",
  "quote",
- "rustc_version 0.4.1",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -702,14 +742,20 @@ dependencies = [
 
 [[package]]
 name = "fslock"
-version = "0.1.8"
+version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "57eafdd0c16f57161105ae1b98a1238f97645f2f588438b2949c99a2af9616bf"
+checksum = "04412b8935272e3a9bae6f48c7bfff74c2911f60525404edfdd28e49884c3bfb"
 dependencies = [
  "libc",
  "winapi",
 ]
 
+[[package]]
+name = "funty"
+version = "2.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6d5a32815ae3f33302d95fdcb2ce17862f8c65363dcfd29360480ba1001fc9c"
+
 [[package]]
 name = "futures"
 version = "0.3.30"
@@ -766,7 +812,7 @@ checksum = "87750cf4b7a4c0625b1529e4c543c2182106e4dedc60a2a6455e00d212c489ac"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -852,6 +898,15 @@ version = "0.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
 
+[[package]]
+name = "gzip-header"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "95cc527b92e6029a62960ad99aa8a6660faa4555fe5f731aab13aa6a921795a2"
+dependencies = [
+ "crc32fast",
+]
+
 [[package]]
 name = "half"
 version = "2.4.1"
@@ -873,7 +928,7 @@ dependencies = [
  "pest_derive",
  "serde",
  "serde_json",
- "thiserror",
+ "thiserror 1.0.63",
 ]
 
 [[package]]
@@ -911,9 +966,9 @@ dependencies = [
 
 [[package]]
 name = "hts-sys"
-version = "2.1.4"
+version = "2.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e9f348d14cb4e50444e39fcd6b00302fe2ed2bc88094142f6278391d349a386d"
+checksum = "e38d7f1c121cd22aa214cb4dadd4277dc5447391eac518b899b29ba6356fbbb2"
 dependencies = [
  "bindgen",
  "bzip2-sys",
@@ -1185,6 +1240,15 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "memoffset"
+version = "0.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a"
+dependencies = [
+ "autocfg",
+]
+
 [[package]]
 name = "minimal-lexical"
 version = "0.2.1"
@@ -1224,13 +1288,12 @@ dependencies = [
 
 [[package]]
 name = "nalgebra"
-version = "0.32.6"
+version = "0.33.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b5c17de023a86f59ed79891b2e5d5a94c705dbe904a5b5c9c952ea6221b03e4"
+checksum = "26aecdf64b707efd1310e3544d709c5c0ac61c13756046aaaba41be5c4f66a3b"
 dependencies = [
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  "matrixmultiply",
- "nalgebra-macros",
  "num-complex",
  "num-rational",
  "num-traits",
@@ -1240,17 +1303,6 @@ dependencies = [
  "typenum",
 ]
 
-[[package]]
-name = "nalgebra-macros"
-version = "0.2.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
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-dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.77",
-]
-
 [[package]]
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 version = "0.1.6"
@@ -1305,6 +1357,7 @@ version = "0.4.2"
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 checksum = "f83d14da390562dca69fc84082e73e548e1ad308d24accdedd2720017cb37824"
 dependencies = [
+ "num-bigint",
  "num-integer",
  "num-traits",
 ]
@@ -1438,7 +1491,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "fdbef9d1d47087a895abd220ed25eb4ad973a5e26f6a4367b038c25e28dfc2d9"
 dependencies = [
  "memchr",
- "thiserror",
+ "thiserror 1.0.63",
  "ucd-trie",
 ]
 
@@ -1462,7 +1515,7 @@ dependencies = [
  "pest_meta",
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -1499,7 +1552,7 @@ checksum = "2f38a4412a78282e09a2cf38d195ea5420d15ba0602cb375210efbc877243965"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -1548,6 +1601,16 @@ dependencies = [
  "zerocopy",
 ]
 
+[[package]]
+name = "prettyplease"
+version = "0.2.27"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "483f8c21f64f3ea09fe0f30f5d48c3e8eefe5dac9129f0075f76593b4c1da705"
+dependencies = [
+ "proc-macro2",
+ "syn",
+]
+
 [[package]]
 name = "proc-macro-rules"
 version = "0.4.0"
@@ -1556,7 +1619,7 @@ checksum = "07c277e4e643ef00c1233393c673f655e3672cf7eb3ba08a00bdd0ea59139b5f"
 dependencies = [
  "proc-macro-rules-macros",
  "proc-macro2",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -1568,14 +1631,14 @@ dependencies = [
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  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
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-version = "1.0.86"
+version = "1.0.92"
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-checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77"
+checksum = "37d3544b3f2748c54e147655edb5025752e2303145b5aefb3c3ea2c78b973bb0"
 dependencies = [
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 ]
@@ -1604,6 +1667,12 @@ dependencies = [
  "proc-macro2",
 ]
 
+[[package]]
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+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dc33ff2d4973d518d823d61aa239014831e521c75da58e3df4840d3f47749d09"
+
 [[package]]
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 version = "0.8.5"
@@ -1757,14 +1826,14 @@ checksum = "6c20b6793b5c2fa6553b250154b78d6d0db37e72700ae35fad9387a46f487c97"
 
 [[package]]
 name = "rust-htslib"
-version = "0.47.0"
+version = "0.49.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "41f1796800e73ebb282c6fc5c03f1fe160e867e01114a58a7e115ee3c1d02482"
+checksum = "115ae57b89deb942275566eca8c31da053d8df0d8bda12e50c4c4aa994877068"
 dependencies = [
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  "custom_derive",
- "derive-new 0.5.9",
+ "derive-new 0.7.0",
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  "ieee754",
  "lazy_static",
@@ -1773,7 +1842,7 @@ dependencies = [
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  "newtype_derive",
  "regex",
- "thiserror",
+ "thiserror 2.0.9",
  "url",
 ]
 
@@ -1807,15 +1876,6 @@ dependencies = [
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 ]
 
-[[package]]
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-source = "registry+https://github.com/rust-lang/crates.io-index"
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-dependencies = [
- "semver 1.0.23",
-]
-
 [[package]]
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 version = "0.38.37"
@@ -1887,12 +1947,6 @@ dependencies = [
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 ]
 
-[[package]]
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-version = "1.0.23"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b"
-
 [[package]]
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 version = "0.7.0"
@@ -1916,7 +1970,7 @@ checksum = "243902eda00fad750862fc144cea25caca5e20d615af0a81bee94ca738f1df1f"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -1934,16 +1988,14 @@ dependencies = [
 
 [[package]]
 name = "serde_v8"
-version = "0.141.0"
+version = "0.220.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bc689cb316d67b200e9f7449ce76cceb7e483e0f828d1a9c3d057c4367b6c26e"
+checksum = "6e7a65d91d79acc82aa229aeb084f4a39bda269069bc1520df40f679495388e4"
 dependencies = [
- "bytes",
- "derive_more",
  "num-bigint",
  "serde",
  "smallvec",
- "thiserror",
+ "thiserror 1.0.63",
  "v8",
 ]
 
@@ -1975,9 +2027,9 @@ dependencies = [
 
 [[package]]
 name = "simba"
-version = "0.8.1"
+version = "0.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "061507c94fc6ab4ba1c9a0305018408e312e17c041eb63bef8aa726fa33aceae"
+checksum = "b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa"
 dependencies = [
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  "num-complex",
@@ -2052,14 +2104,16 @@ dependencies = [
 
 [[package]]
 name = "sourcemap"
-version = "7.1.1"
+version = "8.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e7768edd06c02535e0d50653968f46e1e0d3aa54742190d35dd9466f59de9c71"
+checksum = "208d40b9e8cad9f93613778ea295ed8f3c2b1824217c6cfc7219d3f6f45b96d4"
 dependencies = [
  "base64-simd",
+ "bitvec",
  "data-encoding",
  "debugid",
  "if_chain",
+ "rustc-hash",
  "rustc_version 0.2.3",
  "serde",
  "serde_json",
@@ -2076,11 +2130,17 @@ dependencies = [
  "lock_api",
 ]
 
+[[package]]
+name = "static_assertions"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f"
+
 [[package]]
 name = "statrs"
-version = "0.17.1"
+version = "0.18.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f697a07e4606a0a25c044de247e583a330dbb1731d11bc7350b81f48ad567255"
+checksum = "2a3fe7c28c6512e766b0874335db33c94ad7b8f9054228ae1c2abd47ce7d335e"
 dependencies = [
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  "nalgebra",
@@ -2116,7 +2176,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -2129,7 +2189,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -2144,9 +2204,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "1.0.109"
+version = "2.0.95"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
+checksum = "46f71c0377baf4ef1cc3e3402ded576dccc315800fbc62dfc7fe04b009773b4a"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -2154,15 +2214,10 @@ dependencies = [
 ]
 
 [[package]]
-name = "syn"
-version = "2.0.77"
+name = "tap"
+version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9f35bcdf61fd8e7be6caf75f429fdca8beb3ed76584befb503b1569faee373ed"
-dependencies = [
- "proc-macro2",
- "quote",
- "unicode-ident",
-]
+checksum = "55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369"
 
 [[package]]
 name = "thiserror"
@@ -2170,7 +2225,16 @@ version = "1.0.63"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c0342370b38b6a11b6cc11d6a805569958d54cfa061a29969c3b5ce2ea405724"
 dependencies = [
- "thiserror-impl",
+ "thiserror-impl 1.0.63",
+]
+
+[[package]]
+name = "thiserror"
+version = "2.0.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f072643fd0190df67a8bab670c20ef5d8737177d6ac6b2e9a236cb096206b2cc"
+dependencies = [
+ "thiserror-impl 2.0.9",
 ]
 
 [[package]]
@@ -2181,7 +2245,18 @@ checksum = "a4558b58466b9ad7ca0f102865eccc95938dca1a74a856f2b57b6629050da261"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
+]
+
+[[package]]
+name = "thiserror-impl"
+version = "2.0.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7b50fa271071aae2e6ee85f842e2e28ba8cd2c5fb67f11fcb1fd70b276f9e7d4"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
 ]
 
 [[package]]
@@ -2262,7 +2337,7 @@ checksum = "693d596312e88961bc67d7f1f97af8a70227d9f90c31bba5806eec004978d752"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]
@@ -2436,14 +2511,19 @@ dependencies = [
 
 [[package]]
 name = "v8"
-version = "0.81.0"
+version = "0.106.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b75f5f378b9b54aff3b10da8170d26af4cfd217f644cf671badcd13af5db4beb"
+checksum = "a381badc47c6f15acb5fe0b5b40234162349ed9d4e4fd7c83a7f5547c0fc69c5"
 dependencies = [
- "bitflags 1.3.2",
+ "bindgen",
+ "bitflags 2.6.0",
  "fslock",
+ "gzip-header",
+ "home",
+ "miniz_oxide 0.7.4",
  "once_cell",
- "which",
+ "paste",
+ "which 6.0.3",
 ]
 
 [[package]]
@@ -2482,6 +2562,18 @@ dependencies = [
  "rustix",
 ]
 
+[[package]]
+name = "which"
+version = "6.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b4ee928febd44d98f2f459a4a79bd4d928591333a494a10a868418ac1b39cf1f"
+dependencies = [
+ "either",
+ "home",
+ "rustix",
+ "winsafe",
+]
+
 [[package]]
 name = "wide"
 version = "0.7.28"
@@ -2587,6 +2679,21 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
 
+[[package]]
+name = "winsafe"
+version = "0.0.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d135d17ab770252ad95e9a872d365cf3090e3be864a34ab46f48555993efc904"
+
+[[package]]
+name = "wyz"
+version = "0.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed"
+dependencies = [
+ "tap",
+]
+
 [[package]]
 name = "xmlparser"
 version = "0.13.6"
@@ -2617,7 +2724,7 @@ checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.77",
+ "syn",
 ]
 
 [[package]]

Cargo.toml

@@ -9,7 +9,7 @@ env_logger = "0.11.5"
 indicatif = "0.17.8"
 log = "0.4.22"
 rayon = "1.10.0"
-rust-htslib = "0.47.0"
+rust-htslib = "0.49.0"
 uuid = { version = "1.10.0", features = ["v4"] }
 pandora_lib_graph = { git = "https://git.t0m4.fr/Thomas/pandora_lib_graph.git" }
 indicatif-log-bridge = "0.2.2"
@@ -17,7 +17,7 @@ serde = { version = "1.0.*", default-features = false }
 csv = "1.3.0"
 dashmap = { version = "6.0.1", features = ["rayon"] }
 serde_json = "1.0.128"
-statrs = "0.17.1"
+statrs = "0.18.0"
 rand = "0.8.5"
 indexmap = "2.5.0"
-charming = { version = "0.3.1", features = ["ssr"] }
+charming = { version = "0.4.0", features = ["ssr"] }