diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 029426105d..c50d4e6266 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,7 +10,7 @@ repos: - id: check-toml - id: debug-statements - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.1 + rev: v0.8.2 hooks: - id: ruff-format - id: ruff diff --git a/Cargo.lock b/Cargo.lock index 7c1d93d734..9c45cfc7c8 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -991,13 +991,12 @@ checksum = "a2983372caf4480544083767bf2d27defafe32af49ab4df3a0b7fc90793a3664" [[package]] name = "nalgebra" -version = "0.32.5" +version = "0.33.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3ea4908d4f23254adda3daa60ffef0f1ac7b8c3e9a864cf3cc154b251908a2ef" +checksum = "26aecdf64b707efd1310e3544d709c5c0ac61c13756046aaaba41be5c4f66a3b" dependencies = [ "approx", "matrixmultiply", - "nalgebra-macros", "num-complex", "num-rational", "num-traits", @@ -1007,17 +1006,6 @@ dependencies = [ "typenum", ] -[[package]] -name = "nalgebra-macros" -version = "0.2.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "91761aed67d03ad966ef783ae962ef9bbaca728d2dd7ceb7939ec110fffad998" -dependencies = [ - "proc-macro2", - "quote", - "syn 1.0.104", -] - [[package]] name = "needletail" version = "0.5.1" @@ -1034,9 +1022,9 @@ dependencies = [ [[package]] name = "needletail" -version = "0.6.0" +version = "0.6.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f29a3c5015d6985f33318d154fa0c41315eb2e7df29432c844c74a83434bfe21" +checksum = "de3de09e373770238e3d30eb1a9f09f4754134d0ef354d0570bc1203d2517257" dependencies = [ "buffer-redux", "bytecount", @@ -1459,9 +1447,9 @@ dependencies = [ [[package]] name = "roaring" -version = "0.10.7" +version = "0.10.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f81dc953b2244ddd5e7860cb0bb2a790494b898ef321d4aff8e260efab60cc88" +checksum = "395b0c39c00f9296f3937624c1fa4e0ee44f8c0e4b2c49408179ef381c6c2e6e" dependencies = [ "bytemuck", "byteorder", @@ -1610,9 +1598,9 @@ checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64" [[package]] name = "simba" -version = "0.8.1" +version = "0.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "061507c94fc6ab4ba1c9a0305018408e312e17c041eb63bef8aa726fa33aceae" +checksum = "b3a386a501cd104797982c15ae17aafe8b9261315b5d07e3ec803f2ea26be0fa" dependencies = [ "approx", "num-complex", @@ -1664,7 +1652,7 @@ dependencies = [ "md5", "memmap2", "murmurhash3", - "needletail 0.6.0", + "needletail 0.6.1", "niffler", "nohash-hasher", "num-iter", @@ -1684,7 +1672,7 @@ dependencies = [ "statrs", "streaming-stats", "tempfile", - "thiserror 2.0.3", + "thiserror 2.0.6", "twox-hash", "typed-builder", "vec-collections", @@ -1701,9 +1689,9 @@ checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f" [[package]] name = "statrs" -version = "0.17.1" +version = "0.18.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f697a07e4606a0a25c044de247e583a330dbb1731d11bc7350b81f48ad567255" +checksum = "2a3fe7c28c6512e766b0874335db33c94ad7b8f9054228ae1c2abd47ce7d335e" dependencies = [ "approx", "nalgebra", @@ -1781,11 +1769,11 @@ dependencies = [ [[package]] name = "thiserror" -version = "2.0.3" +version = "2.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c006c85c7651b3cf2ada4584faa36773bd07bac24acfb39f3c431b36d7e667aa" +checksum = "8fec2a1820ebd077e2b90c4df007bebf344cd394098a13c563957d0afc83ea47" dependencies = [ - "thiserror-impl 2.0.3", + "thiserror-impl 2.0.6", ] [[package]] @@ -1801,9 +1789,9 @@ dependencies = [ [[package]] name = "thiserror-impl" -version = "2.0.3" +version = "2.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f077553d607adc1caf65430528a576c757a71ed73944b66ebb58ef2bbd243568" +checksum = "d65750cab40f4ff1929fb1ba509e9914eb756131cef4210da8d5d700d26f6312" dependencies = [ "proc-macro2", "quote", diff --git a/doc/databases.md b/doc/databases.md index 781d2a6f66..3d607bdb9f 100644 --- a/doc/databases.md +++ b/doc/databases.md @@ -30,6 +30,25 @@ The databases do not need to be unpacked or prepared in any way after download. You can verify that they've been successfully downloaded (and view database properties such as `ksize` and `scaled`) with `sourmash sig summarize `. +## Sketches for human and animal genomes + +These sketches are of the latest releases of a number of animal +genomes. Among other uses, they can be used to detect host +contamination in microbial metagenomes. + +Each file includes sketches at k=21, k=31, and k=51, at a scaled of +1000, and is about 110 MB. + +* Human (hg38) - [hg38.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/hg38.sig.zip) +* Cow (bosTau9) - [bosTau9.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/bosTau9.sig.zip) +* Dog (canFam6) - [canFam6.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/canFam6.sig.zip) +* Horse (equCab3) - [equCab3.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/equCab3.sig.zip) +* Cat (felCat9) - [felCat9.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/felCat9.sig.zip) +* Chicken (galGAl6) - [galGal6.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/galGal6.sig.zip) +* Mouse (mm39) - [mm39.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/mm39.sig.zip) +* Goat (oviAri4) - [oviAri4.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/oviAri4.sig.zip) +* Pig (susCr11) - [susScr11.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/susScr11.sig.zip) + ## GTDB R08-RS214 - DNA databases [GTDB R08-RS214](https://forum.gtdb.ecogenomic.org/t/announcing-gtdb-r08-rs214/456) consists of 402,709 genomes organized into 85,205 species clusters. diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml index fcf6bccd23..41cf944fac 100644 --- a/src/core/Cargo.toml +++ b/src/core/Cargo.toml @@ -43,7 +43,7 @@ log = "0.4.22" md5 = "0.7.0" memmap2 = "0.9.5" murmurhash3 = "0.0.5" -needletail = { version = "0.6.0", default-features = false } +needletail = { version = "0.6.1", default-features = false } niffler = { version = "2.4.0", default-features = false, features = [ "gz" ] } nohash-hasher = "0.2.0" num-iter = "0.1.45" @@ -53,11 +53,11 @@ piz = "0.5.0" primal-check = "0.3.4" rayon = { version = "1.10.0", optional = true } rkyv = { version = "0.7.44", optional = true } -roaring = "0.10.7" +roaring = "0.10.8" roots = "0.0.8" serde = { version = "1.0.215", features = ["derive"] } serde_json = "1.0.133" -statrs = "0.17.1" +statrs = "0.18.0" streaming-stats = "0.2.3" thiserror = "2.0" twox-hash = "1.6.0"