diff --git a/Cargo.lock b/Cargo.lock index 0d8b97c..bab7d0d 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -25,9 +25,9 @@ checksum = "5d2e7343e7fc9de883d1b0341e0b13970f764c14101234857d2ddafa1cb1cac2" [[package]] name = "aho-corasick" -version = "0.7.6" +version = "1.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "58fb5e95d83b38284460a5fda7d6470aa0b8844d283a0b614b8535e880800d2d" +checksum = "0f2135563fb5c609d2b2b87c1e8ce7bc41b0b45430fa9661f457981503dd5bf0" dependencies = [ "memchr", ] @@ -101,6 +101,12 @@ dependencies = [ "windows-sys", ] +[[package]] +name = "anyhow" +version = "1.0.75" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6" + [[package]] name = "approx" version = "0.3.2" @@ -173,18 +179,20 @@ dependencies = [ [[package]] name = "bio" -version = "0.30.0" +version = "1.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cc0376f0882981c7440386b060ce1c5fdccf789f2e1e58fb3539745d19d449bd" +checksum = "ea643e25059ce02b94e8f6eb4e902d160baa6d0beb91834ed971dd5a880c02ba" dependencies = [ + "anyhow", "approx", - "bio-types", + "bio-types 1.0.1", "bit-set", "bv", "bytecount", "csv", "custom_derive", - "fnv", + "editdistancek", + "enum-map", "fxhash", "getset", "itertools", @@ -197,14 +205,15 @@ dependencies = [ "num-traits 0.2.15", "ordered-float", "petgraph", - "quick-error", + "rand 0.8.5", "regex", "serde", "serde_derive", - "snafu", "statrs", "strum", - "strum_macros 0.16.0", + "strum_macros", + "thiserror", + "triple_accel", "vec_map", ] @@ -218,7 +227,20 @@ dependencies = [ "lazy_static", "quick-error", "regex", - "strum_macros 0.20.1", + "strum_macros", +] + +[[package]] +name = "bio-types" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9d45749b87f21808051025e9bf714d14ff4627f9d8ca967eade6946ea769aa4a" +dependencies = [ + "derive-new", + "lazy_static", + "regex", + "strum_macros", + "thiserror", ] [[package]] @@ -484,7 +506,7 @@ checksum = "71f31892cd5c62e414316f2963c5689242c43d8e7bbcaaeca97e5e28c95d91d9" dependencies = [ "proc-macro2 1.0.64", "quote 1.0.29", - "syn 1.0.11", + "syn 1.0.109", ] [[package]] @@ -499,10 +521,10 @@ dependencies = [ ] [[package]] -name = "doc-comment" -version = "0.3.1" +name = "editdistancek" +version = "1.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "923dea538cea0aa3025e8685b20d6ee21ef99c4f77e954a30febbaac5ec73a97" +checksum = "3e02df23d5b1c6f9e69fa603b890378123b93073df998a21e6e33b9db0a32613" [[package]] name = "either" @@ -510,6 +532,26 @@ version = "1.5.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "bb1f6b1ce1c140482ea30ddd3335fc0024ac7ee112895426e0a629a6c20adfe3" +[[package]] +name = "enum-map" +version = "1.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e893a7ba6116821058dec84a6fb14fb2a97cd8ce5fd0f85d5a4e760ecd7329d9" +dependencies = [ + "enum-map-derive", +] + +[[package]] +name = "enum-map-derive" +version = "0.6.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "84278eae0af6e34ff6c1db44c11634a694aafac559ff3080e4db4e4ac35907aa" +dependencies = [ + "proc-macro2 1.0.64", + "quote 1.0.29", + "syn 1.0.109", +] + [[package]] name = "equivalent" version = "1.0.1" @@ -555,7 +597,7 @@ checksum = "aa4da3c766cd7a0db8242e326e9e4e081edd567072893ed320008189715366a4" dependencies = [ "proc-macro2 1.0.64", "quote 1.0.29", - "syn 1.0.11", + "syn 1.0.109", "synstructure", ] @@ -591,12 +633,6 @@ dependencies = [ "miniz_oxide 0.3.2", ] -[[package]] -name = "fnv" -version = "1.0.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2fad85553e09a6f881f739c29f0b00b0f01357c743266d478b68951ce23285f3" - [[package]] name = "fs-utils" version = "1.1.1" @@ -640,7 +676,7 @@ checksum = "5bb3f5b7d8d70c9bd23cf29b2b38094661418fb0ea79f1b0cc2019a11d6f5429" dependencies = [ "proc-macro2 1.0.64", "quote 1.0.29", - "syn 1.0.11", + "syn 1.0.109", ] [[package]] @@ -890,9 +926,9 @@ checksum = "60302e4db3a61da70c0cb7991976248362f30319e88850c487b9b95bbf059e00" [[package]] name = "memchr" -version = "2.5.0" +version = "2.6.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d" +checksum = "8f232d6ef707e1956a43342693d2a31e72989554d58299d7a88738cc95b0d35c" [[package]] name = "memoffset" @@ -1041,9 +1077,9 @@ dependencies = [ [[package]] name = "ordered-float" -version = "1.1.1" +version = "3.9.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3305af35278dd29f46fcdd139e0b1fbfae2153f0e5928b39b035542dd31e37b7" +checksum = "2a54938017eacd63036332b4ae5c8a49fc8c0c1d6d629893057e4f13609edd06" dependencies = [ "num-traits 0.2.15", ] @@ -1087,6 +1123,12 @@ version = "0.3.16" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "72d5370d90f49f70bd033c3d75e87fc529fbfff9d6f7cccef07d6170079d91ea" +[[package]] +name = "ppv-lite86" +version = "0.2.17" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de" + [[package]] name = "proc-macro2" version = "0.4.30" @@ -1137,7 +1179,7 @@ checksum = "6d71dacdc3c88c1fde3885a3be3fbab9f35724e6ce99467f7d9c5026132184ca" dependencies = [ "autocfg 0.1.6", "libc", - "rand_chacha", + "rand_chacha 0.1.1", "rand_core 0.4.2", "rand_hc", "rand_isaac", @@ -1148,6 +1190,17 @@ dependencies = [ "winapi", ] +[[package]] +name = "rand" +version = "0.8.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404" +dependencies = [ + "libc", + "rand_chacha 0.3.1", + "rand_core 0.6.4", +] + [[package]] name = "rand_chacha" version = "0.1.1" @@ -1158,6 +1211,16 @@ dependencies = [ "rand_core 0.3.1", ] +[[package]] +name = "rand_chacha" +version = "0.3.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88" +dependencies = [ + "ppv-lite86", + "rand_core 0.6.4", +] + [[package]] name = "rand_core" version = "0.3.1" @@ -1173,6 +1236,15 @@ version = "0.4.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9c33a3c44ca05fa6f1807d8e6743f3824e8509beca625669633be0acbdf509dc" +[[package]] +name = "rand_core" +version = "0.6.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c" +dependencies = [ + "getrandom", +] + [[package]] name = "rand_hc" version = "0.1.0" @@ -1301,21 +1373,32 @@ dependencies = [ [[package]] name = "regex" -version = "1.3.1" +version = "1.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dc220bd33bdce8f093101afe22a037b8eb0e5af33592e6a9caafff0d4cb81cbd" +checksum = "697061221ea1b4a94a624f67d0ae2bfe4e22b8a17b6a192afb11046542cc8c47" +dependencies = [ + "aho-corasick", + "memchr", + "regex-automata", + "regex-syntax", +] + +[[package]] +name = "regex-automata" +version = "0.3.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c2f401f4955220693b56f8ec66ee9c78abffd8d1c4f23dc41a23839eb88f0795" dependencies = [ "aho-corasick", "memchr", "regex-syntax", - "thread_local", ] [[package]] name = "regex-syntax" -version = "0.6.12" +version = "0.7.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "11a7e20d1cce64ef2fed88b66d347f88bd9babb82845b2b858f3edbf59a4f716" +checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da" [[package]] name = "rust-argon2" @@ -1334,7 +1417,7 @@ version = "0.36.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b6d2e5f7980deaf4f41366a5b0d51c2cadaf8639bb12d1258fdab87f37007bd9" dependencies = [ - "bio-types", + "bio-types 0.10.0", "custom_derive", "derefable", "derive-new", @@ -1345,7 +1428,7 @@ dependencies = [ "linear-map", "newtype_derive", "regex", - "strum_macros 0.20.1", + "strum_macros", "thiserror", "url", ] @@ -1459,28 +1542,6 @@ dependencies = [ "maybe-uninit", ] -[[package]] -name = "snafu" -version = "0.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9d0bf93d08d6a44363b47d737f1f5bebbf5e6a1eaaa3d4c128ceeaca6b718292" -dependencies = [ - "backtrace", - "doc-comment", - "snafu-derive", -] - -[[package]] -name = "snafu-derive" -version = "0.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "624e94bd38e471f67883b467711e7a7ad7dbe284f5fb7e661dc8a671fc5b26a0" -dependencies = [ - "proc-macro2 0.4.30", - "quote 0.6.13", - "syn 0.15.44", -] - [[package]] name = "sprs" version = "0.7.1" @@ -1499,7 +1560,7 @@ version = "0.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "835a1669368b3524d9214cfcb274a1f5e3b0820b5f275c1509bfb0cc67664636" dependencies = [ - "rand", + "rand 0.6.5", ] [[package]] @@ -1514,18 +1575,6 @@ version = "0.16.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "6138f8f88a16d90134763314e3fc76fa3ed6a7db4725d6acf9a3ef95a3188d22" -[[package]] -name = "strum_macros" -version = "0.16.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0054a7df764039a6cd8592b9de84be4bec368ff081d203a7d5371cbfa8e65c81" -dependencies = [ - "heck", - "proc-macro2 1.0.64", - "quote 1.0.29", - "syn 1.0.11", -] - [[package]] name = "strum_macros" version = "0.20.1" @@ -1535,7 +1584,7 @@ dependencies = [ "heck", "proc-macro2 1.0.64", "quote 1.0.29", - "syn 1.0.11", + "syn 1.0.109", ] [[package]] @@ -1551,13 +1600,13 @@ dependencies = [ [[package]] name = "syn" -version = "1.0.11" +version = "1.0.109" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dff0acdb207ae2fe6d5976617f887eb1e35a2ba52c13c7234c790960cdad9238" +checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237" dependencies = [ "proc-macro2 1.0.64", "quote 1.0.29", - "unicode-xid 0.2.0", + "unicode-ident", ] [[package]] @@ -1579,7 +1628,7 @@ checksum = "f36bdaa60a83aca3921b5259d5400cbf5e90fc51931376a9bd4a0eb79aa7210f" dependencies = [ "proc-macro2 1.0.64", "quote 1.0.29", - "syn 1.0.11", + "syn 1.0.109", "unicode-xid 0.2.0", ] @@ -1644,16 +1693,7 @@ checksum = "bd80fc12f73063ac132ac92aceea36734f04a1d93c1240c6944e23a3b8841793" dependencies = [ "proc-macro2 1.0.64", "quote 1.0.29", - "syn 1.0.11", -] - -[[package]] -name = "thread_local" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c6b53e329000edc2b34dbe8545fd20e55a333362d0a321909685a19bd28c3f1b" -dependencies = [ - "lazy_static", + "syn 1.0.109", ] [[package]] @@ -1701,6 +1741,12 @@ dependencies = [ "winnow", ] +[[package]] +name = "triple_accel" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "22048bc95dfb2ffd05b1ff9a756290a009224b60b2f0e7525faeee7603851e63" + [[package]] name = "unicode-bidi" version = "0.3.4"