From 489d4cfccd304d7b32c101c67db0303695307e01 Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Wed, 23 Aug 2023 13:26:15 +1200 Subject: [PATCH 1/2] . --- minimappers2/Cargo.lock | 1179 +++++++++++++++++++-------------------- minimappers2/Cargo.toml | 14 +- minimappers2/src/lib.rs | 147 +++-- 3 files changed, 640 insertions(+), 700 deletions(-) diff --git a/minimappers2/Cargo.lock b/minimappers2/Cargo.lock index 67adf46..d2d08f5 100644 --- a/minimappers2/Cargo.lock +++ b/minimappers2/Cargo.lock @@ -2,6 +2,15 @@ # It is not intended for manual editing. version = 3 +[[package]] +name = "addr2line" +version = "0.21.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8a30b2e23b9e17a9f90641c7ab1549cd9b44f296d3ccbf309d2863cfe398a0cb" +dependencies = [ + "gimli", +] + [[package]] name = "adler" version = "1.0.2" @@ -10,12 +19,11 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "ahash" -version = "0.8.2" +version = "0.8.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bf6ccdb167abbf410dcb915cabd428929d7f6a04980b54a11f26a39f1c7f7107" +checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f" dependencies = [ "cfg-if", - "const-random", "getrandom", "once_cell", "version_check", @@ -23,13 +31,25 @@ dependencies = [ [[package]] name = "aho-corasick" -version = "0.7.20" +version = "1.0.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac" +checksum = "6748e8def348ed4d14996fa801f4122cd763fff530258cdc03f64b25f89d3a5a" dependencies = [ "memchr", ] +[[package]] +name = "allocator-api2" +version = "0.2.16" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5" + +[[package]] +name = "android-tzdata" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0" + [[package]] name = "android_system_properties" version = "0.1.5" @@ -40,10 +60,13 @@ dependencies = [ ] [[package]] -name = "anyhow" -version = "1.0.68" +name = "argminmax" +version = "0.6.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2cb2f989d18dd141ab8ae82f64d1a8cdd37e0840f73a406896cf5e99502fab61" +checksum = "202108b46429b765ef483f8a24d5c46f48c14acfdacc086dd4ab6dddf6bcdbd2" +dependencies = [ + "num-traits", +] [[package]] name = "array-init-cursor" @@ -63,9 +86,9 @@ dependencies = [ [[package]] name = "arrow2" -version = "0.16.0" +version = "0.17.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7a4c5b03335bc1cb0fd9f5297f8fd3bbfd6fb04f3cb0bc7d6c91b7128cb8336a" +checksum = "59c468daea140b747d781a1da9f7db5f0a8e6636d4af20cc539e43d05b0604fa" dependencies = [ "ahash", "arrow-format", @@ -75,79 +98,120 @@ dependencies = [ "either", "ethnum", "foreign_vec", + "futures", "getrandom", "hash_hasher", "lexical-core", "lz4", "multiversion", "num-traits", + "regex", + "regex-syntax 0.6.29", "rustc_version", "simdutf8", "strength_reduce", "zstd", ] +[[package]] +name = "async-trait" +version = "0.1.73" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bc00ceb34980c03614e35a3a4e218276a0a824e911d07651cd0d858a51e8c0f0" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.29", +] + +[[package]] +name = "atoi" +version = "2.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f28d99ec8bfea296261ca1af174f24225171fea9664ba9003cbebee704810528" +dependencies = [ + "num-traits", +] + [[package]] name = "autocfg" version = "1.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa" +[[package]] +name = "backtrace" +version = "0.3.69" 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"hashbrown", + "multiversion", + "num-traits", + "polars-error", "thiserror", + "version_check", ] [[package]] name = "polars-core" -version = "0.27.2" +version = "0.32.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5a440cd53916f1a87fac1fda36cd7cc2d226247b4d4570d96242da5fa7f07b2a" +checksum = "b24f92fc5b167f668ff85ab9607dfa72e2c09664cacef59297ee8601dee60126" dependencies = [ "ahash", - "anyhow", "arrow2", - "bitflags", + "bitflags 2.4.0", "chrono", "comfy-table", - "hashbrown 0.13.2", + "either", + "hashbrown", "indexmap", - "num", + "num-traits", "once_cell", "polars-arrow", + "polars-error", + "polars-row", "polars-utils", "rand", "rand_distr", @@ -1177,46 +1053,62 @@ dependencies = [ "regex", "smartstring", "thiserror", - "wasm-timer", + "version_check", "xxhash-rust", ] +[[package]] +name = "polars-error" +version = "0.32.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = 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= "1f2bc9a12da9ed043fb0cb51dbcb87b365e4845b7ab6399d7a81e838460c6974" dependencies = [ - "crossbeam-channel", "enum_dispatch", - "hashbrown 0.13.2", - "num", + "hashbrown", + "num-traits", "polars-arrow", "polars-core", "polars-io", "polars-ops", "polars-plan", + "polars-row", "polars-utils", "rayon", "smartstring", + "version_check", ] [[package]] name = "polars-plan" -version = "0.27.2" +version = "0.32.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9ca57df4974f25fa0642ae18ef00c0836c5120d4371be77a34d4684173b043c3" +checksum = "fb67b014f0295e8e9dbb84404a91d666d477b3bc248a2ed51bc442833b16da35" dependencies = [ "ahash", + "arrow2", "once_cell", "polars-arrow", "polars-core", @@ -1275,16 +1177,47 @@ dependencies = [ "polars-time", "polars-utils", "rayon", + "regex", + "smartstring", + "strum_macros 0.25.2", + "version_check", +] + +[[package]] +name = "polars-row" +version = "0.32.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "27f54c1956027bf6301948fb4f2837cf6d6b638d8dd1edf3aaeaa19906a986be" +dependencies = [ + "arrow2", + "polars-error", + "polars-utils", +] + +[[package]] +name = "polars-sql" +version = "0.32.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dbfcb15cf8eebd25ea1724109d0153817cd484c6326290585f0736b4e7fcf2f4" +dependencies = [ + "polars-arrow", + "polars-core", + "polars-lazy", + "polars-plan", + "serde", + "serde_json", + "sqlparser", ] [[package]] name = "polars-time" -version = "0.27.2" +version = "0.32.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d961a9ccbe3c739de063fbf78449b3c172baf3379f958769c42ee9c309289786" +checksum = "53f42d2632f5971c9575041d33cbcfb1f996900c40bbf58bc6eb0a0c5efbecea" dependencies = [ + "arrow2", + "atoi", "chrono", - "lexical", "now", "once_cell", "polars-arrow", @@ -1292,17 +1225,24 @@ dependencies = [ "polars-ops", "polars-utils", "regex", + "smartstring", ] [[package]] name = "polars-utils" -version = "0.27.2" +version = "0.32.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a741a3325c544c97c7a9ff57d857f089b60041bd92b06c41582df6940ffaa05b" +checksum = "c326708a370d71dc6e11a8f4bbc10a8479e1c314dc048ba73543b815cd0bf339" dependencies = [ + "ahash", + "hashbrown", + "num-traits", "once_cell", + "polars-error", "rayon", + "smartstring", "sysinfo", + "version_check", ] [[package]] @@ -1311,32 +1251,26 @@ version = "0.2.17" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de" -[[package]] -name = "proc-macro-hack" -version = "0.5.20+deprecated" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dc375e1527247fe1a97d8b7156678dfe7c1af2fc075c9a4db3690ecd2a148068" - [[package]] name = "proc-macro2" -version = "1.0.50" +version = "1.0.66" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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+version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "de3887528ad530ba7bdbb1faa8275ec7a1155a45ffa57c37993960277145d640" +checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e" [[package]] name = "windows_i686_msvc" -version = "0.42.1" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bf4d1122317eddd6ff351aa852118a2418ad4214e6613a50e0191f7004372605" +checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406" [[package]] name = "windows_x86_64_gnu" -version = "0.42.1" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c1040f221285e17ebccbc2591ffdc2d44ee1f9186324dd3e84e99ac68d699c45" +checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e" [[package]] name = "windows_x86_64_gnullvm" -version = "0.42.1" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "628bfdf232daa22b0d64fdb62b09fcc36bb01f05a3939e20ab73aaf9470d0463" +checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc" [[package]] name = "windows_x86_64_msvc" -version = "0.42.1" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "447660ad36a13288b1db4d4248e857b510e8c3a225c822ba4fb748c0aafecffd" +checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538" [[package]] name = "xxhash-rust" @@ -1975,18 +1920,18 @@ checksum = "735a71d46c4d68d71d4b24d03fdc2b98e38cea81730595801db779c04fe80d70" [[package]] name = "zstd" -version = "0.11.2+zstd.1.5.2" +version = "0.12.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "20cc960326ece64f010d2d2107537f26dc589a6573a316bd5b1dba685fa5fde4" +checksum = "1a27595e173641171fc74a1232b7b1c7a7cb6e18222c11e9dfb9888fa424c53c" dependencies = [ "zstd-safe", ] [[package]] name = "zstd-safe" -version = "5.0.2+zstd.1.5.2" +version = 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= ["simde"] } -minimap2-sys = { version = "0.1.10", features = ["simde"] } +minimap2 = { version = "0.1.15", features = ["simde"] } +minimap2-sys = { version = "0.1.15", features = ["simde"] } #minimap2 = { path = "../", features = ["simde"] } #minimap2-sys = { path = "../minimap2-sys", features = ["simde"] } crossbeam = "0.8.2" mimalloc = {version = "0.1.34", default-features = false } -pyo3 = { version = "0.18.1" } -polars = "0.27.2" -pyo3-polars = "0.2.0" +pyo3 = { version = "0.19.2" } +polars = "0.32.1" +pyo3-polars = "0.6.0" [profile.release] opt-level = 3 @@ -33,4 +33,4 @@ debug = true opt-level = 3 [features] -default = ["pyo3/extension-module", "pyo3/abi3-py37"] \ No newline at end of file +default = ["pyo3/extension-module", "pyo3/abi3-py37"] diff --git a/minimappers2/src/lib.rs b/minimappers2/src/lib.rs index 24f7788..0496cc0 100644 --- a/minimappers2/src/lib.rs +++ b/minimappers2/src/lib.rs @@ -1,8 +1,8 @@ use std::num::NonZeroI32; use std::sync::{Arc, Mutex}; -use mimalloc::MiMalloc; use crossbeam::queue::ArrayQueue; +use mimalloc::MiMalloc; use minimap2::*; use minimap2_sys::{mm_set_opt, MM_F_CIGAR}; use polars::{df, prelude::*}; @@ -65,10 +65,6 @@ impl Aligner { /// Map multiple sequences - Multithreaded fn map(&self, py: Python<'_>, seqs: Vec) -> PyResult { - // Get GIL and allow_threads - let gil = Python::acquire_gil(); - let py = gil.python(); - // If single threaded, do not open a new thread... if self.aligner.threads == 1 { let mut mappings = Mappings::default(); @@ -83,73 +79,72 @@ impl Aligner { mappings.push(r) }); } + Ok(PyDataFrame(mappings.to_df().unwrap())) + } else { + let work_queue = Arc::new(Mutex::new(seqs)); + let results_queue = Arc::new(ArrayQueue::>>::new(128)); + let mut thread_handles = Vec::new(); + for i in 0..(self.aligner.threads - 1) { + let work_queue = Arc::clone(&work_queue); + let results_queue = Arc::clone(&results_queue); + + let mut aligner = self.aligner.clone(); + + let handle = std::thread::spawn(move || loop { + let backoff = crossbeam::utils::Backoff::new(); + let work = work_queue.lock().unwrap().pop(); + + match work { + Some(sequence) => { + let mut result = aligner + .map(&sequence.sequence, true, true, None, None) + .expect("Unable to align"); + + result.iter_mut().for_each(|mut r| { + r.query_name = Some(sequence.id.clone()); + }); + + results_queue.push(WorkQueue::Work(result)); + } + None => { + // Means the work queue is empty... + results_queue.push(WorkQueue::Done); + break; + } + } + }); + thread_handles.push(handle); + } - return Ok(PyDataFrame(mappings.to_df().unwrap())); - } - - let work_queue = Arc::new(Mutex::new(seqs)); - let results_queue = Arc::new(ArrayQueue::>>::new(128)); - let mut thread_handles = Vec::new(); - for i in 0..(self.aligner.threads - 1) { - let work_queue = Arc::clone(&work_queue); - let results_queue = Arc::clone(&results_queue); - - let mut aligner = self.aligner.clone(); - - let handle = std::thread::spawn(move || loop { - let backoff = crossbeam::utils::Backoff::new(); - let work = work_queue.lock().unwrap().pop(); - - match work { - Some(sequence) => { - let mut result = aligner - .map(&sequence.sequence, true, true, None, None) - .expect("Unable to align"); - - result.iter_mut().for_each(|mut r| { - r.query_name = Some(sequence.id.clone()); - }); - - results_queue.push(WorkQueue::Work(result)); + let mut mappings = Mappings::default(); + let mut finished_count = 0; + + loop { + py.check_signals()?; + let result = results_queue.pop(); + match result { + Some(WorkQueue::Work(result)) => { + result.into_iter().for_each(|r| mappings.push(r)); + } + Some(WorkQueue::Done) => { + finished_count += 1; + if finished_count == (self.aligner.threads - 1) { + break; + } } None => { - // Means the work queue is empty... - results_queue.push(WorkQueue::Done); - break; + // Probably should be backoff, but let's try this for now... + std::thread::sleep(std::time::Duration::from_millis(100)); } } - }); - thread_handles.push(handle); - } + } - let mut mappings = Mappings::default(); - let mut finished_count = 0; - - loop { - py.check_signals()?; - let result = results_queue.pop(); - match result { - Some(WorkQueue::Work(result)) => { - result.into_iter().for_each(|r| mappings.push(r)); - } - Some(WorkQueue::Done) => { - finished_count += 1; - if finished_count == (self.aligner.threads - 1) { - break; - } - } - None => { - // Probably should be backoff, but let's try this for now... - std::thread::sleep(std::time::Duration::from_millis(100)); - } + for handle in thread_handles { + handle.join().unwrap(); } - } - for handle in thread_handles { - handle.join().unwrap(); + Ok(PyDataFrame(mappings.to_df().unwrap())) } - - Ok(PyDataFrame(mappings.to_df().unwrap())) } // Builder functions @@ -556,18 +551,18 @@ mod tests { #[test] fn test_build_aligners() { map_ont().expect("Failed to build minimap2 aligner"); - map_hifi().expect("Failed to build minimap2 aligner");; - ava_ont().expect("Failed to build minimap2 aligner");; - map_10k().expect("Failed to build minimap2 aligner");; - ava_pb().expect("Failed to build minimap2 aligner");; - asm().expect("Failed to build minimap2 aligner");; - asm5().expect("Failed to build minimap2 aligner");; - asm10().expect("Failed to build minimap2 aligner");; - asm20().expect("Failed to build minimap2 aligner");; - short().expect("Failed to build minimap2 aligner");; - sr().expect("Failed to build minimap2 aligner");; - splice().expect("Failed to build minimap2 aligner");; - cdna().expect("Failed to build minimap2 aligner");; + map_hifi().expect("Failed to build minimap2 aligner"); + ava_ont().expect("Failed to build minimap2 aligner"); + map_10k().expect("Failed to build minimap2 aligner"); + ava_pb().expect("Failed to build minimap2 aligner"); + asm().expect("Failed to build minimap2 aligner"); + asm5().expect("Failed to build minimap2 aligner"); + asm10().expect("Failed to build minimap2 aligner"); + asm20().expect("Failed to build minimap2 aligner"); + short().expect("Failed to build minimap2 aligner"); + sr().expect("Failed to build minimap2 aligner"); + splice().expect("Failed to build minimap2 aligner"); + cdna().expect("Failed to build minimap2 aligner"); } #[test] @@ -588,7 +583,7 @@ mod tests { // Test py new fn let seq = Sequence::new("test", "ACGT"); */ - + // Test Mappings struct // Test default and push fn let mut mappings = Mappings::default(); From 23c8345ee485dbdf0b4845efa335940f0a5d8bad Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Wed, 23 Aug 2023 13:28:40 +1200 Subject: [PATCH 2/2] Update version --- minimappers2/Cargo.toml | 2 +- minimappers2/README.md | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/minimappers2/Cargo.toml b/minimappers2/Cargo.toml index 315c48a..b3e469f 100644 --- a/minimappers2/Cargo.toml +++ b/minimappers2/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "minimappers2" -version = "0.1.3" +version = "0.1.4" edition = "2021" [lib] diff --git a/minimappers2/README.md b/minimappers2/README.md index 83e9e3b..40a749d 100644 --- a/minimappers2/README.md +++ b/minimappers2/README.md @@ -111,7 +111,9 @@ and/or: > *Bioinformatics*, **37**:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2] # Changelog -## 0.1.1 UNRELEASED +## 0.1.4 +* Update pyo3, polars, and minimap2-rs deps +## 0.1.1 * Update pyo3 and polars deps * Add with_seq for indexing TODO