diff --git a/Cargo.lock b/Cargo.lock index e0b7778588c..1e41a9ffd6c 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" @@ -5972,21 +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" @@ -6004,35 +5983,38 @@ dependencies = [ [[package]] name = "noodles-core" -version = "0.18.0" +version = "0.19.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8ebfc6396fb51059c98a35bb81b96422ac41ea1bc60b6c8e9c6b2550212e9493" +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", - "noodles-bgzf 0.44.0", + "noodles-bgzf", "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", - "noodles-bgzf 0.44.0", + "noodles-bgzf", "noodles-core", "noodles-csi", "tokio", @@ -6040,14 +6022,14 @@ 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", - "noodles-bgzf 0.44.0", + "noodles-bgzf", "noodles-core", "noodles-csi", "noodles-tabix", @@ -9826,7 +9808,7 @@ dependencies = [ "indicatif", "itertools 0.14.0", "mimalloc", - "noodles-bgzf 0.46.0", + "noodles-bgzf", "noodles-vcf", "parking_lot", "parquet", @@ -10457,7 +10439,7 @@ 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..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 = "0.82.0" +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?;