From 2aa0fd4fd5be250d6c0aef1805e2f14e5de447ed Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 25 Sep 2023 21:45:52 +0000 Subject: [PATCH 1/4] build(deps): bump the noodles group with 1 update Bumps the noodles group with 1 update: [noodles-vcf](https://github.com/zaeleus/noodles). - [Commits](https://github.com/zaeleus/noodles/compare/noodles-vcf-0.39.0...noodles-vcf-0.40.0) --- updated-dependencies: - dependency-name: noodles-vcf dependency-type: direct:production update-type: version-update:semver-minor dependency-group: noodles ... Signed-off-by: dependabot[bot] --- Cargo.lock | 19 +++++++++++++++++-- Cargo.toml | 2 +- 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 50de374a..f8aba5fe 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -280,7 +280,7 @@ dependencies = [ "noodles-core", "noodles-csi", "noodles-tabix", - "noodles-vcf", + "noodles-vcf 0.39.0", "prost", "prost-build", "rayon", @@ -1778,7 +1778,7 @@ dependencies = [ "noodles-csi", "noodles-fasta", "noodles-tabix", - "noodles-vcf", + "noodles-vcf 0.40.0", "parse-display", "pretty_assertions", "procfs", @@ -2002,6 +2002,21 @@ dependencies = [ "percent-encoding", ] +[[package]] +name = "noodles-vcf" +version = "0.40.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dcd62cddca514dd04a13d3f4bf4ff83b5c7bca63c8e6b9ae0de2186ea6517a48" +dependencies = [ + "indexmap 2.0.0", + "memchr", + "noodles-bgzf", + "noodles-core", + "noodles-csi", + "noodles-tabix", + "percent-encoding", +] + [[package]] name = "nu-ansi-term" version = "0.46.0" diff --git a/Cargo.toml b/Cargo.toml index 88ce38a5..7aace27b 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -52,7 +52,7 @@ noodles-core = "0.12" noodles-csi = "0.24" noodles-fasta = "0.29" noodles-tabix = "0.29" -noodles-vcf = "0.39" +noodles-vcf = "0.40" parse-display = "0.8" procfs = "0.15" prost = "0.12" From 4e0a9ebe1d15ff4fcc2b1f775bbca354240ada8d Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 2 Oct 2023 13:39:15 +0200 Subject: [PATCH 2/4] bump annonars to 0.21 --- Cargo.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.toml b/Cargo.toml index 7aace27b..5406f41c 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -27,7 +27,7 @@ path = "src/main.rs" [dependencies] actix-web = "4.4" -annonars = "0.20" +annonars = "0.21" anyhow = "1.0" bgzip = "0.3" bio = "1.3" From 2f4acb15bf5ebe7aea360db263992c322afd57b9 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 2 Oct 2023 13:55:37 +0200 Subject: [PATCH 3/4] wip --- Cargo.lock | 43 ++++++++----------------------------------- 1 file changed, 8 insertions(+), 35 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index f8aba5fe..f50ad56f 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -255,9 +255,9 @@ dependencies = [ [[package]] name = "annonars" -version = "0.20.0" +version = "0.21.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "856d2a30152c991d240d14a38c724f0f800e65d44a5b9ea34279cd67a9e6f912" +checksum = "fe254418f47df5e2ca6dadf365aa55865d8e9740388422faf3e81b64729ba337" dependencies = [ "actix-web", "anyhow", @@ -280,7 +280,7 @@ dependencies = [ "noodles-core", "noodles-csi", "noodles-tabix", - "noodles-vcf 0.39.0", + "noodles-vcf", "prost", "prost-build", "rayon", @@ -1778,7 +1778,7 @@ dependencies = [ "noodles-csi", "noodles-fasta", "noodles-tabix", - "noodles-vcf 0.40.0", + "noodles-vcf", "parse-display", "pretty_assertions", "procfs", @@ -1987,21 +1987,6 @@ dependencies = [ "noodles-csi", ] -[[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", - "noodles-core", - "noodles-csi", - "noodles-tabix", - "percent-encoding", -] - [[package]] name = "noodles-vcf" version = "0.40.0" @@ -2067,16 +2052,6 @@ dependencies = [ "libm", ] -[[package]] -name = "num_cpus" -version = "1.16.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43" -dependencies = [ - "hermit-abi", - "libc", -] - [[package]] name = "number_prefix" version = "0.4.0" @@ -2501,9 +2476,9 @@ checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3" [[package]] name = "rayon" -version = "1.7.0" +version = "1.8.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1d2df5196e37bcc87abebc0053e20787d73847bb33134a69841207dd0a47f03b" +checksum = "9c27db03db7734835b3f53954b534c91069375ce6ccaa2e065441e07d9b6cdb1" dependencies = [ "either", "rayon-core", @@ -2511,14 +2486,12 @@ dependencies = [ [[package]] name = "rayon-core" -version = "1.11.0" +version = "1.12.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4b8f95bd6966f5c87776639160a66bd8ab9895d9d4ab01ddba9fc60661aebe8d" +checksum = "5ce3fb6ad83f861aac485e76e1985cd109d9a3713802152be56c3b1f0e0658ed" dependencies = [ - "crossbeam-channel", "crossbeam-deque", "crossbeam-utils", - "num_cpus", ] [[package]] From 1e198ec38068ef7dc8150225696a66f4362a8163 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 2 Oct 2023 14:25:52 +0200 Subject: [PATCH 4/4] fix tests --- tests/data/annotate/strucvars/example-grch38.vcf | 4 ++-- tests/data/annotate/strucvars/header-grch37-noped.vcf | 4 ++-- tests/data/annotate/strucvars/header-grch37-trio.vcf | 4 ++-- tests/data/annotate/strucvars/header-grch38-noped.vcf | 4 ++-- .../strucvars/maelstrom/delly2-min-with-maelstrom.vcf | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/tests/data/annotate/strucvars/example-grch38.vcf b/tests/data/annotate/strucvars/example-grch38.vcf index db9e7e71..2357b446 100644 --- a/tests/data/annotate/strucvars/example-grch38.vcf +++ b/tests/data/annotate/strucvars/example-grch38.vcf @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:269cd65dac9d34cfd0469e6bae1fbc3c56ce716e6ec2be767bb87620ea98034e -size 5666 +oid sha256:072c790f5e723cf18a270173e945ac7431930a5646abbb362ece703a810da569 +size 5648 diff --git a/tests/data/annotate/strucvars/header-grch37-noped.vcf b/tests/data/annotate/strucvars/header-grch37-noped.vcf index 713d30a5..05cc6d4a 100644 --- a/tests/data/annotate/strucvars/header-grch37-noped.vcf +++ b/tests/data/annotate/strucvars/header-grch37-noped.vcf @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:ef422278360dfa7af198eff4be07764b6a3a1453d33e473c5464cc24ff1cf948 -size 4669 +oid sha256:cea860e0e2ab63f69a9ea8fbb5e81f144f2cd31c7f32ca2b9c965fa44f3187af +size 4651 diff --git a/tests/data/annotate/strucvars/header-grch37-trio.vcf b/tests/data/annotate/strucvars/header-grch37-trio.vcf index 8746c3ed..00b30657 100644 --- a/tests/data/annotate/strucvars/header-grch37-trio.vcf +++ b/tests/data/annotate/strucvars/header-grch37-trio.vcf @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:19f9f4da757a7083532a8149668eb0c17a30d12cb19cc029ea88b25a43fbf706 -size 4956 +oid sha256:abf66786d35dc801f7baa46cf324db3d901c5cc332a6f3d39179c16b4b00e671 +size 4938 diff --git a/tests/data/annotate/strucvars/header-grch38-noped.vcf b/tests/data/annotate/strucvars/header-grch38-noped.vcf index 5b5556e1..f78a7bfc 100644 --- a/tests/data/annotate/strucvars/header-grch38-noped.vcf +++ b/tests/data/annotate/strucvars/header-grch38-noped.vcf @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:cf938ad4052b0bb0b59adc6fa03f5c8431608f01e20a2bdccefbb3ec1693b7cf -size 4676 +oid sha256:c1dbc7c507453ac22a4fbf5aae2ca022fd5d794931414a2c754bd927c55d0c81 +size 4658 diff --git a/tests/data/annotate/strucvars/maelstrom/delly2-min-with-maelstrom.vcf b/tests/data/annotate/strucvars/maelstrom/delly2-min-with-maelstrom.vcf index f09577f4..e625988f 100644 --- a/tests/data/annotate/strucvars/maelstrom/delly2-min-with-maelstrom.vcf +++ b/tests/data/annotate/strucvars/maelstrom/delly2-min-with-maelstrom.vcf @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:33ccbbb691f8201b90584b0ea9dee52858ba8062276fbb08a8668680194efaaa -size 5029 +oid sha256:f9e5785fbc9d04b7d139cf96f9f836cf8a47181045eb00fb8d1d80518645d74e +size 5011