From 0eab05aae4a02bccc977334c331a76b1749cdc92 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 19 Mar 2026 05:15:31 +0000 Subject: [PATCH 1/3] chore(deps): update rust crate noodles-vcf to 0.86.0 --- Cargo.lock | 61 ++++++++++++++++++++++++++++++++++++++++-------------- Cargo.toml | 2 +- 2 files changed, 47 insertions(+), 16 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index e0b7778588c..3088c7d4d16 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -753,12 +753,6 @@ dependencies = [ "syn 2.0.117", ] -[[package]] -name = "bit-vec" -version = "0.8.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5e764a1d40d510daf35e07be9eb06e75770908c27d411ee6c92109c9840eaaf7" - [[package]] name = "bit-vec" version = "0.9.1" @@ -5990,6 +5984,7 @@ dependencies = [ [[package]] name = "noodles-bgzf" version = "0.46.0" +<<<<<<< HEAD source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "37290f565045fd2775b549e62dffca7e1afadc70d8d5a3a2ef19609eb3d8193b" dependencies = [ @@ -6005,34 +6000,62 @@ dependencies = [ [[package]] name = "noodles-core" version = "0.18.0" +======= +>>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8ebfc6396fb51059c98a35bb81b96422ac41ea1bc60b6c8e9c6b2550212e9493" +checksum = "37290f565045fd2775b549e62dffca7e1afadc70d8d5a3a2ef19609eb3d8193b" +dependencies = [ + "bytes", + "crossbeam-channel", + "flate2", + "futures", + "pin-project-lite", + "tokio", + "tokio-util", +] + +[[package]] +name = "noodles-core" +version = "0.19.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "53e1e8a419dbba0e4000b0e60830b124138c7f2277ad556463506f1a81d32d17" dependencies = [ "bstr", ] [[package]] name = "noodles-csi" -version = "0.52.0" +version = "0.55.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d09e31153abd7996f22a50d70f43af6c2ebf96a44ee250326ed15d4e183744c9" +checksum = "c9c846d8128bd80b18d891b13cb9e0bc1d364429d6ab3ec3c83939f3d32ba105" dependencies = [ - "bit-vec 0.8.0", + "bit-vec", "bstr", + "futures", "indexmap", +<<<<<<< HEAD "noodles-bgzf 0.44.0", +======= + "noodles-bgzf 0.46.0", +>>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) "noodles-core", + "pin-project-lite", + "tokio", ] [[package]] name = "noodles-tabix" -version = "0.58.0" +version = "0.61.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3dd8ed06bbf341ce64649717ce0fa1723bf60547eb7d61bd271b79130016dfa4" +checksum = "2443d0852c9618cd4aa8d11bc7c1884285e46aa4466cf5c1e49f3d9756ca7ced" dependencies = [ "bstr", "indexmap", +<<<<<<< HEAD "noodles-bgzf 0.44.0", +======= + "noodles-bgzf 0.46.0", +>>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) "noodles-core", "noodles-csi", "tokio", @@ -6040,14 +6063,18 @@ dependencies = [ [[package]] name = "noodles-vcf" -version = "0.82.0" +version = "0.86.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8d46b26eb1873883e5e6b738c75d4e44c9e1edcc1c6454fc5c25b56202e510bc" +checksum = "0131147080a5aeadcd6c2ab43e7ca1f9e8018cdd482eed797d081c40e8f0a3c7" dependencies = [ "futures", "indexmap", "memchr", +<<<<<<< HEAD "noodles-bgzf 0.44.0", +======= + "noodles-bgzf 0.46.0", +>>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) "noodles-core", "noodles-csi", "noodles-tabix", @@ -9826,7 +9853,11 @@ dependencies = [ "indicatif", "itertools 0.14.0", "mimalloc", +<<<<<<< HEAD "noodles-bgzf 0.46.0", +======= + "noodles-bgzf 0.44.0", +>>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) "noodles-vcf", "parking_lot", "parquet", @@ -10457,7 +10488,7 @@ dependencies = [ "arrow-array", "arrow-schema", "async-trait", - "bit-vec 0.9.1", + "bit-vec", "futures", "itertools 0.14.0", "parking_lot", diff --git a/Cargo.toml b/Cargo.toml index d8d232741c1..c2f71502600 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -173,7 +173,7 @@ mimalloc = "0.1.42" moka = { version = "0.12.10", default-features = false } multiversion = "0.8.0" noodles-bgzf = "0.46.0" -noodles-vcf = "0.82.0" +noodles-vcf = "0.86.0" num-traits = "0.2.19" num_enum = { version = "0.7.3", default-features = false } object_store = { version = "0.12.4", default-features = false } From 31a36db82b6262dab0307d9308a48fab7f98c96a Mon Sep 17 00:00:00 2001 From: Robert Kruszewski Date: Wed, 18 Mar 2026 22:25:12 -0700 Subject: [PATCH 2/3] fixes Signed-off-by: Robert Kruszewski --- Cargo.lock | 31 +++++++++++---------- Cargo.toml | 2 +- vortex-bench/src/statpopgen/download_vcf.rs | 2 +- 3 files changed, 18 insertions(+), 17 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 3088c7d4d16..0a031700157 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -5966,21 +5966,6 @@ dependencies = [ "memchr", ] -[[package]] -name = "noodles-bgzf" -version = "0.44.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7ab0c2585bad37cfc51a55f29c85449400ac51aaade935049d5d9fc5f8add255" -dependencies = [ - "bytes", - "crossbeam-channel", - "flate2", - "futures", - "pin-project-lite", - "tokio", - "tokio-util", -] - [[package]] name = "noodles-bgzf" version = "0.46.0" @@ -6033,11 +6018,15 @@ dependencies = [ "bstr", "futures", "indexmap", +<<<<<<< HEAD <<<<<<< HEAD "noodles-bgzf 0.44.0", ======= "noodles-bgzf 0.46.0", >>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) +======= + "noodles-bgzf", +>>>>>>> 048959940 (fixes) "noodles-core", "pin-project-lite", "tokio", @@ -6051,11 +6040,15 @@ checksum = "2443d0852c9618cd4aa8d11bc7c1884285e46aa4466cf5c1e49f3d9756ca7ced" dependencies = [ "bstr", "indexmap", +<<<<<<< HEAD <<<<<<< HEAD "noodles-bgzf 0.44.0", ======= "noodles-bgzf 0.46.0", >>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) +======= + "noodles-bgzf", +>>>>>>> 048959940 (fixes) "noodles-core", "noodles-csi", "tokio", @@ -6070,11 +6063,15 @@ dependencies = [ "futures", "indexmap", "memchr", +<<<<<<< HEAD <<<<<<< HEAD "noodles-bgzf 0.44.0", ======= "noodles-bgzf 0.46.0", >>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) +======= + "noodles-bgzf", +>>>>>>> 048959940 (fixes) "noodles-core", "noodles-csi", "noodles-tabix", @@ -9853,11 +9850,15 @@ dependencies = [ "indicatif", "itertools 0.14.0", "mimalloc", +<<<<<<< HEAD <<<<<<< HEAD "noodles-bgzf 0.46.0", ======= "noodles-bgzf 0.44.0", >>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) +======= + "noodles-bgzf", +>>>>>>> 048959940 (fixes) "noodles-vcf", "parking_lot", "parquet", diff --git a/Cargo.toml b/Cargo.toml index c2f71502600..0108b152e49 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -173,7 +173,7 @@ mimalloc = "0.1.42" moka = { version = "0.12.10", default-features = false } multiversion = "0.8.0" noodles-bgzf = "0.46.0" -noodles-vcf = "0.86.0" +noodles-vcf = { version = "0.86.0", features = ["async"] } num-traits = "0.2.19" num_enum = { version = "0.7.3", default-features = false } object_store = { version = "0.12.4", default-features = false } diff --git a/vortex-bench/src/statpopgen/download_vcf.rs b/vortex-bench/src/statpopgen/download_vcf.rs index 7d5552541c5..503bf0b0e5f 100644 --- a/vortex-bench/src/statpopgen/download_vcf.rs +++ b/vortex-bench/src/statpopgen/download_vcf.rs @@ -61,7 +61,7 @@ impl StatPopGenBenchmark { let mut bgzf_reader = noodles_bgzf::r#async::io::Reader::new(buf_reader); // Read and parse VCF header - let mut vcf_reader = noodles_vcf::AsyncReader::new(&mut bgzf_reader); + let mut vcf_reader = noodles_vcf::r#async::io::Reader::new(&mut bgzf_reader); // Read and print the first 100,000 records let header = vcf_reader.read_header().await?; From 97e32f176b34eeefb7415c58bb5a735992365afb Mon Sep 17 00:00:00 2001 From: Robert Kruszewski Date: Wed, 18 Mar 2026 22:28:36 -0700 Subject: [PATCH 3/3] lock Signed-off-by: Robert Kruszewski --- Cargo.lock | 50 -------------------------------------------------- 1 file changed, 50 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 0a031700157..1e41a9ffd6c 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -5969,24 +5969,6 @@ dependencies = [ [[package]] name = "noodles-bgzf" version = "0.46.0" -<<<<<<< HEAD -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "37290f565045fd2775b549e62dffca7e1afadc70d8d5a3a2ef19609eb3d8193b" -dependencies = [ - "bytes", - "crossbeam-channel", - "flate2", - "futures", - "pin-project-lite", - "tokio", - "tokio-util", -] - -[[package]] -name = "noodles-core" -version = "0.18.0" -======= ->>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "37290f565045fd2775b549e62dffca7e1afadc70d8d5a3a2ef19609eb3d8193b" dependencies = [ @@ -6018,15 +6000,7 @@ dependencies = [ "bstr", "futures", "indexmap", -<<<<<<< HEAD -<<<<<<< HEAD - "noodles-bgzf 0.44.0", -======= - "noodles-bgzf 0.46.0", ->>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) -======= "noodles-bgzf", ->>>>>>> 048959940 (fixes) "noodles-core", "pin-project-lite", "tokio", @@ -6040,15 +6014,7 @@ checksum = "2443d0852c9618cd4aa8d11bc7c1884285e46aa4466cf5c1e49f3d9756ca7ced" dependencies = [ "bstr", "indexmap", -<<<<<<< HEAD -<<<<<<< HEAD - "noodles-bgzf 0.44.0", -======= - "noodles-bgzf 0.46.0", ->>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) -======= "noodles-bgzf", ->>>>>>> 048959940 (fixes) "noodles-core", "noodles-csi", "tokio", @@ -6063,15 +6029,7 @@ dependencies = [ "futures", "indexmap", "memchr", -<<<<<<< HEAD -<<<<<<< HEAD - "noodles-bgzf 0.44.0", -======= - "noodles-bgzf 0.46.0", ->>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) -======= "noodles-bgzf", ->>>>>>> 048959940 (fixes) "noodles-core", "noodles-csi", "noodles-tabix", @@ -9850,15 +9808,7 @@ dependencies = [ "indicatif", "itertools 0.14.0", "mimalloc", -<<<<<<< HEAD -<<<<<<< HEAD - "noodles-bgzf 0.46.0", -======= - "noodles-bgzf 0.44.0", ->>>>>>> ddf8d96ac (chore(deps): update rust crate noodles-vcf to 0.86.0) -======= "noodles-bgzf", ->>>>>>> 048959940 (fixes) "noodles-vcf", "parking_lot", "parquet",