diff --git a/Cargo.lock b/Cargo.lock index 43705351..489e5478 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -21,17 +21,17 @@ dependencies = [ [[package]] name = "actix-http" -version = "3.3.1" +version = "3.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c2079246596c18b4a33e274ae10c0e50613f4d32a4198e09c7b93771013fed74" +checksum = "a92ef85799cba03f76e4f7c10f533e66d87c9a7e7055f3391f09000ad8351bc9" dependencies = [ "actix-codec", "actix-rt", "actix-service", "actix-utils", - "ahash 0.8.3", + "ahash", "base64", - "bitflags 1.3.2", + "bitflags 2.3.3", "brotli", "bytes", "bytestring", @@ -132,9 +132,9 @@ dependencies = [ [[package]] name = "actix-web" -version = "4.3.1" +version = "4.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cd3cb42f9566ab176e1ef0b8b3a896529062b4efc6be0123046095914c4c1c96" +checksum = "0e4a5b5e29603ca8c94a77c65cf874718ceb60292c5a5c3e5f4ace041af462b9" dependencies = [ "actix-codec", "actix-http", @@ -145,7 +145,7 @@ dependencies = [ "actix-service", "actix-utils", "actix-web-codegen", - "ahash 0.7.6", + "ahash", "bytes", "bytestring", "cfg-if", @@ -154,7 +154,6 @@ dependencies = [ "encoding_rs", "futures-core", "futures-util", - "http", "itoa", "language-tags", "log", @@ -166,7 +165,7 @@ dependencies = [ "serde_json", "serde_urlencoded", "smallvec", - "socket2 0.4.9", + "socket2 0.5.3", "time", "url", ] @@ -198,17 +197,6 @@ version = "1.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" -[[package]] -name = "ahash" -version = "0.7.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47" -dependencies = [ - "getrandom", - "once_cell", - "version_check", -] - [[package]] name = "ahash" version = "0.8.3" @@ -268,9 +256,9 @@ dependencies = [ [[package]] name = "annonars" -version = "0.12.9" +version = "0.17.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "846e14b552e5d2518ee81fbb9e021bdc4dbc72af894a987d8747325ddbefb372" +checksum = "14a57bad32811df7d2bf4d13aebf4337bf8b4b7a5b9264f9ae96b380c6278cb8" dependencies = [ "actix-web", "anyhow", @@ -284,21 +272,21 @@ dependencies = [ "enum-map 2.6.3", "env_logger", "flate2", - "hgvs", + "hgvs 0.10.1", "indexmap 2.0.0", "indicatif", "log", "noodles-bed", - "noodles-bgzf 0.22.0", + "noodles-bgzf 0.23.0", "noodles-core", - "noodles-csi 0.21.0", - "noodles-tabix 0.24.0", - "noodles-vcf 0.33.0", + "noodles-csi 0.23.0", + "noodles-tabix 0.28.0", + "noodles-vcf 0.37.0", "prost 0.11.9", "prost-build 0.11.9", "rayon", "rocksdb", - "rocksdb-utils-lookup", + "rocksdb-utils-lookup 0.2.0", "serde", "serde_json", "serde_with", @@ -310,9 +298,9 @@ dependencies = [ [[package]] name = "annonars" -version = "0.17.0" +version = "0.20.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "14a57bad32811df7d2bf4d13aebf4337bf8b4b7a5b9264f9ae96b380c6278cb8" +checksum = "856d2a30152c991d240d14a38c724f0f800e65d44a5b9ea34279cd67a9e6f912" dependencies = [ "actix-web", "anyhow", @@ -326,21 +314,21 @@ dependencies = [ "enum-map 2.6.3", "env_logger", "flate2", - "hgvs", + "hgvs 0.11.0", "indexmap 2.0.0", "indicatif", "log", "noodles-bed", - "noodles-bgzf 0.23.0", + "noodles-bgzf 0.24.0", "noodles-core", - "noodles-csi 0.23.0", - "noodles-tabix 0.28.0", - "noodles-vcf 0.37.0", - "prost 0.11.9", - "prost-build 0.11.9", + "noodles-csi 0.24.0", + "noodles-tabix 0.29.0", + "noodles-vcf 0.39.0", + "prost 0.12.1", + "prost-build 0.12.0", "rayon", "rocksdb", - "rocksdb-utils-lookup", + "rocksdb-utils-lookup 0.3.0", "serde", "serde_json", "serde_with", @@ -1110,9 +1098,9 @@ dependencies = [ [[package]] name = "equivalent" -version = "1.0.0" +version = "1.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "88bffebc5d80432c9b140ee17875ff173a8ab62faad5b257da912bd2f6c1c0a1" +checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" [[package]] name = "errno" @@ -1406,7 +1394,7 @@ version = "0.14.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2c6201b9ff9fd90a5a3bac2e56a830d0caa509576f0e503818ee82c181b3437a" dependencies = [ - "ahash 0.8.3", + "ahash", "allocator-api2", ] @@ -1454,10 +1442,36 @@ dependencies = [ "md-5", "nom", "postgres", - "quick_cache", + "quick_cache 0.3.0", "regex", "rustc-hash", - "seqrepo", + "seqrepo 0.6.1", + "serde", + "serde_json", + "thiserror", +] + +[[package]] +name = "hgvs" +version = "0.11.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d2c8237412c585364c6d56a985ea67f550a2e8fd55c6b8f949e732a89d2274a7" +dependencies = [ + "base16ct", + "bio", + "chrono", + "enum-map 2.6.3", + "flate2", + "indexmap 2.0.0", + "lazy_static", + "log", + "md-5", + "nom", + "postgres", + "quick_cache 0.4.0", + "regex", + "rustc-hash", + "seqrepo 0.8.0", "serde", "serde_json", "thiserror", @@ -1849,12 +1863,12 @@ dependencies = [ [[package]] name = "mehari" -version = "0.6.2" +version = "0.7.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dcca8876bf33117d3b0d6ee8b16d7795dff0f310f8a047c0733124d1be2076d5" +checksum = "4a26fc67865c0e7536b74f167bc78ed179d21eb28f0c7f0f8dbe9ad20b3dc0a0" dependencies = [ "actix-web", - "annonars 0.12.9", + "annonars 0.20.0", "anyhow", "bgzip", "bio", @@ -1867,29 +1881,29 @@ dependencies = [ "derivative", "env_logger", "flate2", - "hgvs", + "hgvs 0.11.0", "indexmap 2.0.0", "indicatif", "jsonl", "lazy_static", "log", "nom", - "noodles-bgzf 0.22.0", + "noodles-bgzf 0.24.0", "noodles-core", - "noodles-csi 0.21.0", - "noodles-fasta", - "noodles-tabix 0.24.0", - "noodles-vcf 0.33.0", + "noodles-csi 0.24.0", + "noodles-fasta 0.29.0", + "noodles-tabix 0.29.0", + "noodles-vcf 0.39.0", "parse-display", "procfs", - "prost 0.11.9", - "prost-build 0.11.9", - "quick_cache", + "prost 0.12.1", + "prost-build 0.12.0", + "quick_cache 0.4.0", "rand 0.8.5", "rand_core 0.6.4", "rocksdb", "rustc-hash", - "seqrepo", + "seqrepo 0.8.0", "serde", "serde_json", "serde_with", @@ -2062,6 +2076,18 @@ dependencies = [ "flate2", ] +[[package]] +name = "noodles-bgzf" +version = "0.24.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8f4c43ff0879c542c1d8fd570c03e368f629587721d10267f2619e36afc9c9b0" +dependencies = [ + "byteorder", + "bytes", + "crossbeam-channel", + "flate2", +] + [[package]] name = "noodles-core" version = "0.12.0" @@ -2070,27 +2096,27 @@ checksum = "94fbe3192fe33acacabaedd387657f39b0fc606f1996d546db0dfe14703b843a" [[package]] name = "noodles-csi" -version = "0.21.0" +version = "0.23.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f967502cfb925c863664248a844b64f0aa62c9250680e0cd613149932129e67d" +checksum = "8cfc861de7505bfee33662ec69eba023d60eafebf176f08027084c0fa7e69a66" dependencies = [ "bit-vec", "byteorder", - "indexmap 1.9.3", - "noodles-bgzf 0.22.0", + "indexmap 2.0.0", + "noodles-bgzf 0.23.0", "noodles-core", ] [[package]] name = "noodles-csi" -version = "0.23.0" +version = "0.24.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8cfc861de7505bfee33662ec69eba023d60eafebf176f08027084c0fa7e69a66" +checksum = "1b2bb780250c88bc9ea69b56c1aa9df75decc6b79035f3f5ab10c0cd84d24fc6" dependencies = [ "bit-vec", "byteorder", "indexmap 2.0.0", - "noodles-bgzf 0.23.0", + "noodles-bgzf 0.24.0", "noodles-core", ] @@ -2107,16 +2133,15 @@ dependencies = [ ] [[package]] -name = "noodles-tabix" -version = "0.24.0" +name = "noodles-fasta" +version = "0.29.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c2a6c228f3f55a16d58491116b70421cf74c3230609dd0e5433367998dbe2ac1" +checksum = "1012431f881aad1912f9650a8d33e7f7493c6202bc2e889949ec1bc26a55f26d" dependencies = [ - "bit-vec", - "byteorder", - "noodles-bgzf 0.22.0", + "bytes", + "memchr", + "noodles-bgzf 0.24.0", "noodles-core", - "noodles-csi 0.21.0", ] [[package]] @@ -2133,19 +2158,16 @@ dependencies = [ ] [[package]] -name = "noodles-vcf" -version = "0.33.0" +name = "noodles-tabix" +version = "0.29.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dfbf9c613446f62aabc359b779b9b5008463c72a77c289bade19852480be7acc" +checksum = "056e394ddb4c64bcc9806551a69833294062159600aa8ecf7167a922512bda4f" dependencies = [ - "indexmap 1.9.3", - "memchr", - "nom", - "noodles-bgzf 0.22.0", + "bit-vec", + "byteorder", + "noodles-bgzf 0.24.0", "noodles-core", - "noodles-csi 0.21.0", - "noodles-tabix 0.24.0", - "percent-encoding", + "noodles-csi 0.24.0", ] [[package]] @@ -2163,6 +2185,21 @@ dependencies = [ "percent-encoding", ] +[[package]] +name = "noodles-vcf" +version = "0.39.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1a056c06c7b33d5ba10bb59c09cca9500b02c3e0ead964dd4cf8f0068159783a" +dependencies = [ + "indexmap 2.0.0", + "memchr", + "noodles-bgzf 0.24.0", + "noodles-core", + "noodles-csi 0.24.0", + "noodles-tabix 0.29.0", + "percent-encoding", +] + [[package]] name = "nu-ansi-term" version = "0.46.0" @@ -2626,11 +2663,23 @@ version = "0.3.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5253a3a0d56548d5b0be25414171dc780cc6870727746d05bd2bde352eee96c5" dependencies = [ - "ahash 0.8.3", + "ahash", "hashbrown 0.13.2", "parking_lot", ] +[[package]] +name = "quick_cache" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f69f8d22fa3f34f3083d9a4375c038732c7a7e964de1beb81c544da92dfc40b8" +dependencies = [ + "ahash", + "equivalent", + "hashbrown 0.14.0", + "parking_lot", +] + [[package]] name = "quote" version = "1.0.29" @@ -2845,6 +2894,17 @@ dependencies = [ "tracing", ] +[[package]] +name = "rocksdb-utils-lookup" +version = "0.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b83002edb508bf7fc5b234bde1489ccaea5bffbaeaf0aae00270257c858b5f9f" +dependencies = [ + "rocksdb", + "thiserror", + "tracing", +] + [[package]] name = "rstest" version = "0.18.2" @@ -3007,7 +3067,22 @@ dependencies = [ "chrono", "noodles-bgzf 0.22.0", "noodles-core", - "noodles-fasta", + "noodles-fasta 0.25.0", + "rusqlite", + "thiserror", + "tracing", +] + +[[package]] +name = "seqrepo" +version = "0.8.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "94b3579efbd2915e936798fb9f52629feec3cbeef1ef23eb556d49d89ff31455" +dependencies = [ + "chrono", + "noodles-bgzf 0.24.0", + "noodles-core", + "noodles-fasta 0.29.0", "rusqlite", "thiserror", "tracing", @@ -3665,7 +3740,7 @@ dependencies = [ "file_diff", "flate2", "float-cmp", - "hgvs", + "hgvs 0.11.0", "indexmap 2.0.0", "insta", "itertools 0.11.0", diff --git a/Cargo.toml b/Cargo.toml index 46ec77c4..c07e344f 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -25,12 +25,12 @@ csv = "1.1" enum-map = { version = "2.6", features = ["serde"] } fastrand = "2.0" flate2 = "1.0" -hgvs = "0.10" +hgvs = "0.11" indexmap = { version = "2.0", features = ["serde"] } itertools = "0.11" lazy_static = "1.4" log = "0.4" -mehari = "0.6" +mehari = "0.7" multimap = "0.9" procfs = "0.15" prost = "0.12"