From 8c309584173b512a9ae7815d7203a3ede0b96954 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 8 Nov 2023 08:39:49 +0000 Subject: [PATCH] build(deps): bump the noodles group with 3 updates (#274) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Manuel Holtgrewe Release-As: 0.24.5 --- Cargo.lock | 168 +++++++++++++++---------------- Cargo.toml | 6 +- src/freqs/cli/import/reading.rs | 8 +- src/gnomad_nuclear/cli/import.rs | 3 +- src/gnomad_pbs/gnomad2.rs | 6 +- src/gnomad_pbs/gnomad3.rs | 2 +- src/gnomad_pbs/mtdna.rs | 2 +- 7 files changed, 94 insertions(+), 101 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index b2c64de2..5efb0ecb 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -65,7 +65,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e01ed3140b2f8d422c68afa1ed2e85d996ea619c988ac834d255db32138655cb" dependencies = [ "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -178,7 +178,7 @@ dependencies = [ "actix-router", "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -198,9 +198,9 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "ahash" -version = "0.8.4" +version = "0.8.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "72832d73be48bac96a5d7944568f305d829ed55b0ce3b483647089dfaf6cf704" +checksum = "91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a" dependencies = [ "cfg-if", "getrandom", @@ -403,7 +403,7 @@ dependencies = [ "regex", "rustc-hash", "shlex", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -466,9 +466,9 @@ dependencies = [ [[package]] name = "brotli-decompressor" -version = "2.5.0" +version = "2.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "da74e2b81409b1b743f8f0c62cc6254afefb8b8e50bbfe3735550f7aeefa3448" +checksum = "4e2e4afe60d7dd600fdd3de8d0f08c2b7ec039712e3b6137ff98b7004e82de4f" dependencies = [ "alloc-no-stdlib", "alloc-stdlib", @@ -494,9 +494,9 @@ checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223" [[package]] name = "bytestring" -version = "1.3.0" +version = "1.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "238e4886760d98c4f899360c834fa93e62cf7f721ac3c2da375cbdf4b8679aae" +checksum = "74d80203ea6b29df88012294f62733de21cfeab47f17b41af3a38bc30a03ee72" dependencies = [ "bytes", ] @@ -604,7 +604,7 @@ dependencies = [ "heck", "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -657,9 +657,9 @@ checksum = "e496a50fda8aacccc86d7529e2c1e0892dbd0f898a6b5645b5561b89c3210efa" [[package]] name = "cpufeatures" -version = "0.2.10" +version = "0.2.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3fbc60abd742b35f2492f808e1abbb83d45f72db402e14c55057edc9c7b1e9e4" +checksum = "ce420fe07aecd3e67c5f910618fe65e94158f6dcc0adf44e00d69ce2bdfe0fd0" dependencies = [ "libc", ] @@ -768,7 +768,7 @@ dependencies = [ "proc-macro2", "quote", "strsim", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -779,7 +779,7 @@ checksum = "836a9bbc7ad63342d6d6e7b815ccab164bc77a2d95d84bc3117a8c0d5c98e2d5" dependencies = [ "darling_core", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -860,7 +860,7 @@ checksum = "04d0b288e3bb1d861c4403c1774a6f7a798781dfc519b3647df2a3dd4ae95f25" dependencies = [ "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -931,27 +931,27 @@ dependencies = [ [[package]] name = "futures-core" -version = "0.3.28" +version = "0.3.29" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4bca583b7e26f571124fe5b7561d49cb2868d79116cfa0eefce955557c6fee8c" +checksum = "eb1d22c66e66d9d72e1758f0bd7d4fd0bee04cad842ee34587d68c07e45d088c" [[package]] name = "futures-sink" -version = "0.3.28" +version = "0.3.29" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f43be4fe21a13b9781a69afa4985b0f6ee0e1afab2c6f454a8cf30e2b2237b6e" +checksum = "e36d3378ee38c2a36ad710c5d30c2911d752cb941c00c72dbabfb786a7970817" [[package]] name = "futures-task" -version = "0.3.28" +version = "0.3.29" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "76d3d132be6c0e6aa1534069c705a74a5997a356c0dc2f86a47765e5617c5b65" +checksum = "efd193069b0ddadc69c46389b740bbccdd97203899b48d09c5f7969591d6bae2" [[package]] name = "futures-util" -version = "0.3.28" +version = "0.3.29" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "26b01e40b772d54cf6c6d721c1d1abd0647a0106a12ecaa1c186273392a69533" +checksum = "a19526d624e703a3179b3d322efec918b6246ea0fa51d41124525f00f1cc8104" dependencies = [ "futures-core", "futures-task", @@ -1214,9 +1214,9 @@ dependencies = [ [[package]] name = "js-sys" -version = "0.3.64" +version = "0.3.65" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c5f195fe497f702db0f318b07fdd68edb16955aed830df8363d837542f8f935a" +checksum = "54c0c35952f67de54bb584e9fd912b3023117cbafc0a77d8f3dee1fb5f572fe8" dependencies = [ "wasm-bindgen", ] @@ -1241,9 +1241,9 @@ checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55" [[package]] name = "libc" -version = "0.2.149" +version = "0.2.150" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a08173bc88b7955d1b3145aa561539096c421ac8debde8cbc3612ec635fee29b" +checksum = "89d92a4743f9a61002fae18374ed11e7973f530cb3a3255fb354818118b2203c" [[package]] name = "libloading" @@ -1296,9 +1296,9 @@ checksum = "da2479e8c062e40bf0066ffa0bc823de0a9368974af99c9f6df941d2c231e03f" [[package]] name = "local-channel" -version = "0.1.4" +version = "0.1.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e0a493488de5f18c8ffcba89eebb8532ffc562dc400490eb65b84893fae0b178" +checksum = "b6cbc85e69b8df4b8bb8b89ec634e7189099cea8927a276b7384ce5488e53ec8" dependencies = [ "futures-core", "futures-sink", @@ -1307,9 +1307,9 @@ dependencies = [ [[package]] name = "local-waker" -version = "0.1.3" +version = "0.1.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e34f76eb3611940e0e7d53a9aaa4e6a3151f69541a282fd0dad5571420c53ff1" +checksum = "4d873d7c67ce09b42110d801813efbc9364414e356be9935700d368351657487" [[package]] name = "lock_api" @@ -1430,9 +1430,9 @@ checksum = "94fbe3192fe33acacabaedd387657f39b0fc606f1996d546db0dfe14703b843a" [[package]] name = "noodles-csi" -version = "0.25.1" +version = "0.26.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "39d86e55b4784ba7c38b4ffbfc24e122bc05ce971b0a664e8e1a15ffd9de68a7" +checksum = "e0531175d5473e6057c1724c1242b19bfc42dba644fe275b4df89c5b8d31a782" dependencies = [ "bit-vec", "byteorder", @@ -1443,12 +1443,13 @@ dependencies = [ [[package]] name = "noodles-tabix" -version = "0.31.0" +version = "0.32.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d12d6981ba752798cb03abc9604324ff6cbc1e5354252f95c372545d967a6daf" +checksum = "415e319f97784c110a85756a8747bf26e9a18bf321b113d00984ca1af7a6fef9" dependencies = [ "bit-vec", "byteorder", + "indexmap 2.1.0", "noodles-bgzf", "noodles-core", "noodles-csi", @@ -1456,9 +1457,9 @@ dependencies = [ [[package]] name = "noodles-vcf" -version = "0.43.0" +version = "0.45.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f13f0225114584f7ab147f146532dccc584e810006a4dfb275544957e7722884" +checksum = "6000206d1ec762d3c983fb189edde86a22c969de3bb90e4048c4916c492babfa" dependencies = [ "indexmap 2.1.0", "memchr", @@ -1533,7 +1534,7 @@ checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e" dependencies = [ "cfg-if", "libc", - "redox_syscall 0.4.1", + "redox_syscall", "smallvec", "windows-targets 0.48.5", ] @@ -1586,9 +1587,9 @@ checksum = "26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964" [[package]] name = "portable-atomic" -version = "1.5.0" +version = "1.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b559898e0b4931ed2d3b959ab0c2da4d99cc644c4b0b1a35b4d344027f474023" +checksum = "3bccab0e7fd7cc19f820a1c8c91720af652d0c88dc9664dd72aef2614f04af3b" [[package]] name = "powerfmt" @@ -1619,7 +1620,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ae005bd773ab59b4725093fd7df83fd7892f7d8eafb48dbd7de6e024e4215f9d" dependencies = [ "proc-macro2", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -1658,7 +1659,7 @@ dependencies = [ "prost", "prost-types", "regex", - "syn 2.0.38", + "syn 2.0.39", "tempfile", "which", ] @@ -1673,7 +1674,7 @@ dependencies = [ "itertools", "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -1744,15 +1745,6 @@ dependencies = [ "crossbeam-utils", ] -[[package]] -name = "redox_syscall" -version = "0.3.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29" -dependencies = [ - "bitflags 1.3.2", -] - [[package]] name = "redox_syscall" version = "0.4.1" @@ -1835,9 +1827,9 @@ dependencies = [ [[package]] name = "rustix" -version = "0.38.20" +version = "0.38.21" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "67ce50cb2e16c2903e30d1cbccfd8387a74b9d4c938b6a4c5ec6cc7556f7a8a0" +checksum = "2b426b0506e5d50a7d8dafcf2e81471400deb602392c7dd110815afb4eaf02a3" dependencies = [ "bitflags 2.4.1", "errno", @@ -1872,22 +1864,22 @@ checksum = "836fa6a3e1e547f9a2c4040802ec865b5d85f4014efe00555d7090a3dcaa1090" [[package]] name = "serde" -version = "1.0.190" +version = "1.0.192" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "91d3c334ca1ee894a2c6f6ad698fe8c435b76d504b13d436f0685d648d6d96f7" +checksum = "bca2a08484b285dcb282d0f67b26cadc0df8b19f8c12502c13d966bf9482f001" dependencies = [ "serde_derive", ] [[package]] name = "serde_derive" -version = "1.0.190" +version = "1.0.192" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "67c5609f394e5c2bd7fc51efda478004ea80ef42fee983d5c67a65e34f32c0e3" +checksum = "d6c7207fbec9faa48073f3e3074cbe553af6ea512d7c21ba46e434e70ea9fbc1" dependencies = [ "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -1940,7 +1932,7 @@ dependencies = [ "darling", "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -2034,7 +2026,7 @@ dependencies = [ "proc-macro2", "quote", "rustversion", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -2050,9 +2042,9 @@ dependencies = [ [[package]] name = "syn" -version = "2.0.38" +version = "2.0.39" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e96b79aaa137db8f61e26363a0c9b47d8b4ec75da28b7d1d614c2303e232408b" +checksum = "23e78b90f2fcf45d3e842032ce32e3f2d1545ba6636271dcbf24fa306d87be7a" dependencies = [ "proc-macro2", "quote", @@ -2067,13 +2059,13 @@ checksum = "921f1e9c427802414907a48b21a6504ff6b3a15a1a3cf37e699590949ad9befc" [[package]] name = "tempfile" -version = "3.8.0" +version = "3.8.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cb94d2f3cc536af71caac6b6fcebf65860b347e7ce0cc9ebe8f70d3e521054ef" +checksum = "7ef1adac450ad7f4b3c28589471ade84f25f731a7a0fe30d71dfa9f60fd808e5" dependencies = [ "cfg-if", "fastrand", - "redox_syscall 0.3.5", + "redox_syscall", "rustix", "windows-sys 0.48.0", ] @@ -2095,7 +2087,7 @@ checksum = "f66edd6b6cd810743c0c71e1d085e92b01ce6a72782032e3f794c8284fe4bcdd" dependencies = [ "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -2115,7 +2107,7 @@ checksum = "266b2e40bc00e5a6c09c3584011e08b06f123c00362c92b975ba9843aaaa14b8" dependencies = [ "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -2191,9 +2183,9 @@ dependencies = [ [[package]] name = "tokio-util" -version = "0.7.9" +version = "0.7.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1d68074620f57a0b21594d9735eb2e98ab38b17f80d3fcb189fca266771ca60d" +checksum = "5419f34732d9eb6ee4c3578b7989078579b7f039cbbb9ca2c4da015749371e15" dependencies = [ "bytes", "futures-core", @@ -2223,7 +2215,7 @@ checksum = "34704c8d6ebcbc939824180af020566b01a7c01f80641264eba0999f6c2b6be7" dependencies = [ "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] @@ -2337,9 +2329,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423" [[package]] name = "wasm-bindgen" -version = "0.2.87" +version = "0.2.88" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7706a72ab36d8cb1f80ffbf0e071533974a60d0a308d01a5d0375bf60499a342" +checksum = "7daec296f25a1bae309c0cd5c29c4b260e510e6d813c286b19eaadf409d40fce" dependencies = [ "cfg-if", "wasm-bindgen-macro", @@ -2347,24 +2339,24 @@ dependencies = [ [[package]] name = "wasm-bindgen-backend" -version = "0.2.87" +version = "0.2.88" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5ef2b6d3c510e9625e5fe6f509ab07d66a760f0885d858736483c32ed7809abd" +checksum = "e397f4664c0e4e428e8313a469aaa58310d302159845980fd23b0f22a847f217" dependencies = [ "bumpalo", "log", "once_cell", "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", "wasm-bindgen-shared", ] [[package]] name = "wasm-bindgen-macro" -version = "0.2.87" +version = "0.2.88" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dee495e55982a3bd48105a7b947fd2a9b4a8ae3010041b9e0faab3f9cd028f1d" +checksum = "5961017b3b08ad5f3fe39f1e79877f8ee7c23c5e5fd5eb80de95abc41f1f16b2" dependencies = [ "quote", "wasm-bindgen-macro-support", @@ -2372,22 +2364,22 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro-support" -version = "0.2.87" +version = "0.2.88" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b" +checksum = "c5353b8dab669f5e10f5bd76df26a9360c748f054f862ff5f3f8aae0c7fb3907" dependencies = [ "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", "wasm-bindgen-backend", "wasm-bindgen-shared", ] [[package]] name = "wasm-bindgen-shared" -version = "0.2.87" +version = "0.2.88" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ca6ad05a4870b2bf5fe995117d3728437bd27d7cd5f06f13c17443ef369775a1" +checksum = "0d046c5d029ba91a1ed14da14dca44b68bf2f124cfbaf741c54151fdb3e0750b" [[package]] name = "which" @@ -2590,22 +2582,22 @@ checksum = "09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec" [[package]] name = "zerocopy" -version = "0.7.11" +version = "0.7.25" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4c19fae0c8a9efc6a8281f2e623db8af1db9e57852e04cde3e754dd2dc29340f" +checksum = "8cd369a67c0edfef15010f980c3cbe45d7f651deac2cd67ce097cd801de16557" dependencies = [ "zerocopy-derive", ] [[package]] name = "zerocopy-derive" -version = "0.7.11" +version = "0.7.25" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fc56589e9ddd1f1c28d4b4b5c773ce232910a6bb67a70133d61c9e347585efe9" +checksum = "c2f140bda219a26ccc0cdb03dba58af72590c53b22642577d88a927bc5c87d6b" dependencies = [ "proc-macro2", "quote", - "syn 2.0.38", + "syn 2.0.39", ] [[package]] diff --git a/Cargo.toml b/Cargo.toml index 8ebfda60..5d64527f 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -36,9 +36,9 @@ log = "0.4" noodles-bed = "0.10" noodles-bgzf = "0.25" noodles-core = "0.12" -noodles-csi = "0.25" -noodles-tabix = "0.31" -noodles-vcf = "0.43" +noodles-csi = "0.26" +noodles-tabix = "0.32" +noodles-vcf = "0.45" prost = "0.12" rayon = "1.8" rocksdb-utils-lookup = "0.3" diff --git a/src/freqs/cli/import/reading.rs b/src/freqs/cli/import/reading.rs index 51787886..110e63e0 100644 --- a/src/freqs/cli/import/reading.rs +++ b/src/freqs/cli/import/reading.rs @@ -237,7 +237,7 @@ mod test { #[test] fn guess_assembly_helix_chrmt_ambiguous_ok_initial_none() -> Result<(), anyhow::Error> { let path = "tests/freqs/reading/helix.chrM.vcf"; - let mut reader = noodles_vcf::reader::Builder.build_from_path(path)?; + let mut reader = noodles_vcf::reader::Builder::default().build_from_path(path)?; let header = reader.read_header()?; let actual = guess_assembly(&header, true, None)?; @@ -249,7 +249,7 @@ mod test { #[test] fn guess_assembly_helix_chrmt_ambiguous_ok_initial_override() -> Result<(), anyhow::Error> { let path = "tests/freqs/reading/helix.chrM.vcf"; - let mut reader = noodles_vcf::reader::Builder.build_from_path(path)?; + let mut reader = noodles_vcf::reader::Builder::default().build_from_path(path)?; let header = reader.read_header()?; let actual = guess_assembly(&header, true, Some(Assembly::Grch37p10))?; @@ -262,7 +262,7 @@ mod test { fn guess_assembly_helix_chrmt_ambiguous_ok_initial_override_fails() -> Result<(), anyhow::Error> { let path = "tests/freqs/reading/helix.chrM.vcf"; - let mut reader = noodles_vcf::reader::Builder.build_from_path(path)?; + let mut reader = noodles_vcf::reader::Builder::default().build_from_path(path)?; let header = reader.read_header()?; assert!(guess_assembly(&header, false, Some(Assembly::Grch37)).is_err()); @@ -273,7 +273,7 @@ mod test { #[test] fn guess_assembly_helix_chrmt_ambiguous_fail() -> Result<(), anyhow::Error> { let path = "tests/freqs/reading/helix.chrM.vcf"; - let mut reader = noodles_vcf::reader::Builder.build_from_path(path)?; + let mut reader = noodles_vcf::reader::Builder::default().build_from_path(path)?; let header = reader.read_header()?; assert!(guess_assembly(&header, false, None).is_err()); diff --git a/src/gnomad_nuclear/cli/import.rs b/src/gnomad_nuclear/cli/import.rs index be99772b..06239a39 100644 --- a/src/gnomad_nuclear/cli/import.rs +++ b/src/gnomad_nuclear/cli/import.rs @@ -250,7 +250,8 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> tracing::info!("Opening gnomAD-nuclear VCF file..."); let before_loading = std::time::Instant::now(); - let mut reader_vcf = noodles_vcf::reader::Builder.build_from_path(&args.path_in_vcf[0])?; + let mut reader_vcf = + noodles_vcf::reader::Builder::default().build_from_path(&args.path_in_vcf[0])?; let header = reader_vcf.read_header()?; let vep_version = if let Some(record::value::Collection::Unstructured(values)) = header diff --git a/src/gnomad_pbs/gnomad2.rs b/src/gnomad_pbs/gnomad2.rs index a0e4fcc6..6726819b 100644 --- a/src/gnomad_pbs/gnomad2.rs +++ b/src/gnomad_pbs/gnomad2.rs @@ -434,7 +434,7 @@ mod test { #[test] fn test_record_from_vcf_allele_gnomad_exomes_grch37() -> Result<(), anyhow::Error> { let path_vcf = "tests/gnomad-nuclear/example-exomes-grch37/gnomad-exomes.vcf"; - let mut reader_vcf = noodles_vcf::reader::Builder.build_from_path(path_vcf)?; + let mut reader_vcf = noodles_vcf::reader::Builder::default().build_from_path(path_vcf)?; let header = reader_vcf.read_header()?; let mut records = Vec::new(); @@ -453,7 +453,7 @@ mod test { #[test] fn test_record_from_vcf_allele_gnomad_genomes_grch37() -> Result<(), anyhow::Error> { let path_vcf = "tests/gnomad-nuclear/example-genomes-grch37/gnomad-genomes.vcf"; - let mut reader_vcf = noodles_vcf::reader::Builder.build_from_path(path_vcf)?; + let mut reader_vcf = noodles_vcf::reader::Builder::default().build_from_path(path_vcf)?; let header = reader_vcf.read_header()?; let mut records = Vec::new(); @@ -472,7 +472,7 @@ mod test { #[test] fn test_record_from_vcf_allele_gnomad_exomes_grch38() -> Result<(), anyhow::Error> { let path_vcf = "tests/gnomad-nuclear/example-exomes-grch38/gnomad-exomes.vcf"; - let mut reader_vcf = noodles_vcf::reader::Builder.build_from_path(path_vcf)?; + let mut reader_vcf = noodles_vcf::reader::Builder::default().build_from_path(path_vcf)?; let header = reader_vcf.read_header()?; let mut records = Vec::new(); diff --git a/src/gnomad_pbs/gnomad3.rs b/src/gnomad_pbs/gnomad3.rs index 313b64cc..05f15573 100644 --- a/src/gnomad_pbs/gnomad3.rs +++ b/src/gnomad_pbs/gnomad3.rs @@ -407,7 +407,7 @@ mod test { #[test] fn test_record_from_vcf_allele_gnomad_genomes_grch38() -> Result<(), anyhow::Error> { let path_vcf = "tests/gnomad-nuclear/example-genomes-grch38/gnomad-genomes.vcf"; - let mut reader_vcf = noodles_vcf::reader::Builder.build_from_path(path_vcf)?; + let mut reader_vcf = noodles_vcf::reader::Builder::default().build_from_path(path_vcf)?; let header = reader_vcf.read_header()?; let mut records = Vec::new(); diff --git a/src/gnomad_pbs/mtdna.rs b/src/gnomad_pbs/mtdna.rs index f352a281..1b1141e5 100644 --- a/src/gnomad_pbs/mtdna.rs +++ b/src/gnomad_pbs/mtdna.rs @@ -308,7 +308,7 @@ mod test { #[test] fn test_record_from_vcf_allele() -> Result<(), anyhow::Error> { let path_vcf = "tests/gnomad-mtdna/example/gnomad-mtdna.vcf"; - let mut reader_vcf = noodles_vcf::reader::Builder.build_from_path(path_vcf)?; + let mut reader_vcf = noodles_vcf::reader::Builder::default().build_from_path(path_vcf)?; let header = reader_vcf.read_header()?; let mut records = Vec::new();