update-to-minimap2-2.29

CHANGELOG.md

@@ -1,3 +1,9 @@
+### 0.1.24 minimap2 2.29
++ Update minimap2-sys to 2.29
++ Rust 2024 edition 
++ Remove best_n setting to 1, it should be determined by minimap2
++ Helper functions for read_junction, read_pass1, read_splice_scores
+
 ### 0.1.23 minimap2 2.28
 + Functions to set flag opts for MapOpt and IdxOpt @dwpeng
 + Fixed memory leak when not dropping mm_idx_t properly. This is done by adding in syntactic sugar in minimap2-sys @jguhlin

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "minimap2"
-version = "0.1.23+minimap2.2.28"
-edition = "2021"
+version = "0.1.24+minimap2.2.29"
+edition = "2024"
 authors = ["Joseph Guhlin <[email protected]>"]
 license = "MIT OR Apache-2.0"
 description = "Bindings to libminimap2"
@@ -29,7 +29,7 @@ exclude = ["minimappers2", "fakeminimap2", "minimap2-sys"]
 libc = "0.2"
 needletail = { version = "0.6", optional = true, default-features = false}
 
-minimap2-sys = { path = "./minimap2-sys" , version = "0.1.21+minimap2.2.28" }
+minimap2-sys = { path = "./minimap2-sys", version = "0.1.22+minimap2.2.29" }
 rust-htslib = { version = "0.49", default-features = false, optional = true }
 
 [dev-dependencies]

README.md

@@ -11,23 +11,19 @@ minimap2-sys is the raw FFI bindings to minimap2. minimap2 is the more opinionat
 # How to use
 ## Requirements
 ```toml
-minimap2 = "0.1.23+minimap2.2.28"
+minimap2 = "0.1.24+minimap2.2.29"
 ```
 Also see [Features](#features)
 
 Tested with rustc 1.82.0 and nightly. So probably a good idea to upgrade before running. But let me know if you run into pain points with older versions and will try to fix.
 
 ## Minimap2 Version Table
-| minimap2-rs | minimap2 |
-|-------------|----------|
-| 0.1.23      | 2.28     |
-| 0.1.22      | 2.28     |
-| 0.1.21      | 2.28     |
-| 0.1.20      | 2.28     |
-| 0.1.19      | 2.28     |
-| 0.1.18      | 2.28     |
-| 0.1.17      | 2.27     |
-| 0.1.16      | 2.26     |
+| minimap2-rs     | minimap2 |
+|-----------------|----------|
+| 0.1.24          | 2.29     |
+| 0.1.18 - 0.1.23 | 2.28     |
+| 0.1.17          | 2.27     |
+| 0.1.16          | 2.26     |
 
 ## Usage
 Create an Aligner 
@@ -184,6 +180,19 @@ Minimap2 is tested on x86_64 and aarch64 (arm64). Other platforms may work, plea
 - [STRdust](https://github.com/wdecoster/STRdust) - Tandem repeat genotyper for long reads
 - [oarfish](https://github.com/COMBINE-lab/oarfish) - transcript quantification from long-read RNA-seq data
 - [lrge](https://github.com/mbhall88/lrge) - Long Read-based Genome size Estimation from overlaps
+- [mmr](https://github.com/arcInstitute/mmr) - A minimap2-based aligner with BINSEQ file format support
+
+# Notes
+## Memory management
+Minimap2 sets cap_kalloc to ~500Mb, so for 32 threads this can be ~16Gb. You can set this manually with `aligner.mapopt.cap_kalloc`. This is a good idea if you are using a lot of threads, or have very long running jobs.
+
+```
+    let per_thread_cap_kalloc = (1_000_000_000_f64 / (args.threads as f64)).ceil() as i64;
+    aligner.mapopt.cap_kalloc = per_thread_cap_kalloc;
+```
+
+## best_n
+* Minimap2 outputs and results are sensitive to the best_n parameter. Set it manually or be prepared for it to be changed upstream (potentially!)
 
 # Next things todo
 * Iterator interface for map_file

examples/channels.rs

@@ -1,6 +1,6 @@
 use crossbeam::queue::ArrayQueue;
 use minimap2::*;
-use needletail::{parse_fastx_file, FastxReader};
+use needletail::{FastxReader, parse_fastx_file};
 
 use std::path::PathBuf;
 use std::{error::Error, path::Path, sync::Arc, time::Duration};
@@ -99,16 +99,16 @@ fn map(
 
         let handle = std::thread::spawn(move || {
             // Now that the threads are running, read the input file and push the work to the queue
-            let mut reader: Box<dyn FastxReader> =
-                parse_fastx_file(query_file).unwrap_or_else(|_| panic!("Can't find query FASTA file"));
+            let mut reader: Box<dyn FastxReader> = parse_fastx_file(query_file)
+                .unwrap_or_else(|_| panic!("Can't find query FASTA file"));
 
             // I just do this in the main thread, but you can split threads
             let backoff = crossbeam::utils::Backoff::new();
             while let Some(Ok(record)) = reader.next() {
                 let mut work = WorkQueue::Work((record.id().to_vec(), record.seq().to_vec()));
                 while let Err(work_packet) = work_queue.push(work) {
                     work = work_packet; // Simple way to maintain ownership
-                                        // If we have an error, it's 99% because the queue is full
+                    // If we have an error, it's 99% because the queue is full
                     backoff.snooze();
                 }
             }
@@ -128,7 +128,6 @@ fn map(
             // This is where we processs mapping results as they come in...
             Some(WorkQueue::Result((record, alignments))) => {
                 num_alignments += alignments.len();
-
             }
             Some(_) => unimplemented!("Unexpected result type"),
             None => {
@@ -178,7 +177,7 @@ fn worker(
                 let mut result = WorkQueue::Result((sequence, alignment));
                 while let Err(result_packet) = results_queue.push(result) {
                     result = result_packet; // Simple way to maintain ownership
-                                            // If we have an error, it's 99% because the queue is full
+                    // If we have an error, it's 99% because the queue is full
                     backoff.snooze();
                 }
             }

examples/rayon.rs

@@ -1,7 +1,7 @@
+use clap::Parser;
 use minimap2::*;
-use needletail::{parse_fastx_file, FastxReader};
+use needletail::{FastxReader, parse_fastx_file};
 use rayon::prelude::*;
-use clap::Parser;
 
 use std::path::PathBuf;
 use std::{error::Error, path::Path};

minimap2-sys/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "minimap2-sys"
-version = "0.1.21+minimap2.2.28"
-edition = "2021"
+version = "0.1.22+minimap2.2.29"
+edition = "2024"
 links = "libminimap2"
 authors = ["Joseph Guhlin <[email protected]>"]
 license = "MIT OR Apache-2.0"
@@ -26,7 +26,6 @@ exclude = [
 	"/mm2-fast/test",
 	"/minimap2/test",
 	"/mm2-fast/test_bench/",
-
 ]
 
 [lib]

minimap2-sys/README.md

@@ -5,6 +5,10 @@ Use this if you need lower-level bindings for minimap2.
 Minimap2 2.28
 
 ## Breaking Changes
+### 0.1.29
+Potentially an issue, derive(copy) is no longer valid for structs where we have implemented a Drop trait. So I've added some newtypes where appropriate. Hopefully it's an invisible change.
+This is primarily for mm_idx_t. If you use it directly (instead of MmIdx newtype), you need to call mm_idx_destroy() manually.
+
 ### 0.1.18
 mm2-fast and minimap2 have diverged. At this point mm2-fast is no longer supported. Please use a previous crate version.
 
@@ -19,6 +23,12 @@ mm2-fast and minimap2 have diverged. At this point mm2-fast is no longer support
 * Can we decouple from pthread? This would allow Windows and (possibly) WASM compilation.
 
 ## Changelog
+### 0.1.29 minimap2.2.29
+* Update to minimap2 2.29
+* Update to 2024 edition
+* Remove some noise from the build system
+* Remove Drop impl for mm_idx_t. If you use it directly (instead of MmIdx newtype), you need to call mm_idx_destroy() manually.
+
 ### 0.1.21 minimap2.2.28
 * Flag functions for IdxOpt and MapOpt @dwpeng
 * Syntactic sugar for mm_idx_t to support Drop, Deref, and DerefMut

minimap2-sys/build.rs

@@ -1,3 +1,4 @@
+
 use std::env;
 use std::path::{Path, PathBuf};
 
@@ -124,6 +125,8 @@ fn simde(cc: &mut cc::Build) {
 
 fn compile() {
     let mut cc = cc::Build::new();
+    cc.warnings(false);
+    cc.flag_if_supported("-Wno-unused-result");
 
     let out_path = PathBuf::from(env::var_os("OUT_DIR").unwrap());
 
@@ -148,7 +151,8 @@ fn compile() {
     cc.flag("-lz");
 
     let mut cc = cc::Build::new();
-
+
+    cc.flag_if_supported("-Wno-unused-result");
     cc.warnings(false);
     cc.flag("-Wc++-compat");
     cc.out_dir(&out_path);
@@ -206,6 +210,7 @@ fn gen_bindings() {
     let out_path = PathBuf::from(env::var_os("OUT_DIR").unwrap());
 
     let mut bindgen = bindgen::Builder::default()
+        .derive_debug(true)
         .parse_callbacks(Box::new(bindgen::CargoCallbacks::new()))
         .rustfmt_bindings(true);