#71 move drop to minimap2-sys

impl Drop for mm_idx_t {
    fn drop(&mut self) {
        unsafe { mm_idx_destroy(self) };
    }
}

.gitignore

@@ -7,3 +7,4 @@ test_data/*.bam
 test_data/*.mmi
 .ipynb_checkpoints
 .vscode/
+.quarto

Cargo.toml

@@ -50,13 +50,14 @@ rayon = "1.10"
 
 [features]
 default = ["map-file"]
-sse2only = ["minimap2-sys/sse2only"]
+map-file = ["needletail"] #, "simdutf8"]
 htslib = ['rust-htslib']
 simde = ["minimap2-sys/simde"]
-map-file = ["needletail"] #, "simdutf8"]
 zlib-ng = ["minimap2-sys/zlib-ng"]
 curl = ["rust-htslib/curl"]
 static = ["minimap2-sys/static", "rust-htslib/static"]
+sse2only = ["minimap2-sys/sse2only"]
+
 
 [package.metadata.docs.rs]
 features = ["map-file", "htslib"]

README.md

@@ -6,20 +6,21 @@ A rust FFI library for [minimap2](https://github.com/lh3/minimap2/). In developm
 [![codecov](https://codecov.io/gh/jguhlin/minimap2-rs/branch/main/graph/badge.svg?token=huw27ZC6Qy)](https://codecov.io/gh/jguhlin/minimap2-rs)
 
 # Structure
-minimap2-sys is the library of the raw FFI bindings to minimap2. minimap2 is the more rusty version.
+minimap2-sys is the raw FFI bindings to minimap2. minimap2 is the more opinionated, rusty version.
 
 # How to use
 ## Requirements
 ```toml
-minimap2 = "0.1.20+minimap2.2.28"
+minimap2 = "0.1.21+minimap2.2.28"
 ```
 Also see [Features](#features)
 
-Tested with rustc 1.64.0 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!
+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 |
 |-------------|----------|
+| 0.1.21      | 2.28     |
 | 0.1.20      | 2.28     |
 | 0.1.19      | 2.28     |
 | 0.1.18      | 2.28     |
@@ -117,19 +118,21 @@ let results = sequences.par_iter().map(|seq| {
 
 ## Features
 The following crate features are available:
-* `mm2-fast` - Replace minimap2 with [mm2-fast](https://github.com/bwa-mem2/mm2-fast). This is likely not portable.
-* `htslib` - Support output of bam/sam files using htslib.
-* `simde` - Compile minimap2 / mm2-fast with [simd-everywhere](https://github.com/simd-everywhere/simde) support. 
-* `map-file` - *Default* - Convenience function for mapping an entire file. Caution, this is single-threaded. 
-* `sse2only` - Compiles for SSE2 support only (Default is to try to compile for SSE4.1, SSE2 only is default on aarch64)
+* map-file - Enables the ability to map a file directly to a reference. Enabled by deafult
+* htslib - Provides an interface to minimap2 that returns rust_htslib::Records
+* simde - Enables SIMD Everywhere library in minimap2
+* zlib-ng - Enables the use of zlib-ng for faster compression
+* curl - Enables curl for htslib
+* static - Builds minimap2 as a static library
+* sse2only - Builds minimap2 with only SSE2 support
 
 Map-file is a *default* feature and enabled unless otherwise specified.
 
 ## Missing Features
 * setting mismatch penalty for base transitions [minimap 2.27 release notes](https://github.com/lh3/minimap2/releases/tag/v2.27)
 * Generate ds tags to indicate uncertainty in indels
 
-Potentially more, but I'm using this to keep track. I'd expect those would get implemented over time, but if you have urgent need open a pull request or an issue! Thanks
+Potentially others. Please create an issue! 
 
 ## Building for MUSL
 Follow these [instructions](https://github.com/rust-cross/rust-musl-cross#prebuilt-images).
@@ -141,10 +144,9 @@ alias rust-musl-builder='docker run --rm -it -v "$(pwd)":/home/rust/src messense
 rust-musl-builder cargo build --release
 ```
 
-Please note minimap2 is only tested for x86_64. Other platforms may work, please open an issue if minimap2 compiles but minimap2-rs does not.
+Minimap2 is tested on x86_64 and aarch64 (arm64). Other platforms may work, please open an issue if minimap2 compiles but minimap2-rs does not.
 
 ### Features tested with MUSL
-* `mm2-fast` - **Fail**
 * `htslib` - **Success**
 * `simde` - **Success**
 
@@ -153,23 +155,19 @@ Please note minimap2 is only tested for x86_64. Other platforms may work, please
 - [mappy-rs](https://github.com/Adoni5/mappy-rs) - Drop-in multi-threaded replacement for python's mappy
 - [HiFiHLA](https://github.com/PacificBiosciences/hifihla) - HLA star-calling tool for PacBio HiFi data
 - [STRdust](https://github.com/wdecoster/STRdust) - Tandem repeat genotyper for long reads
-
-# Want feedback
-* Many fields are i32 / i8 to mimic the C environment, but would it make more sense to convert to u32 / u8 / usize?
-* Let me know pain points!
+- [oarfish](https://github.com/COMBINE-lab/oarfish) - transcript quantification from long-read RNA-seq data
 
 # Next things todo
-* Print other tags so we can have an entire PAF format
-* -sys Compile with SSE2 / SSE4.1 (auto-detect, but also make with features)
 * Multi-thread guide (tokio async threads or use crossbeam queue and traditional threads?)
 * Iterator interface for map_file
-* MORE TESTS
-* -sys Get SSE working with "sse" feature (compiles and tests work in -sys crate, but not main crate)
 * -sys Possible to decouple from pthread?
-* -sys Enable Lisa-hash for mm2-fast? But must handle build arguments from the command-line.
 
 # Citation
-You should cite the minimap2 papers if you use this in your work.
+Please cite the appropriate minimap2 papers if you use this in your work, as well as this library.
+
+## DOI for this library
+
+## Minimap2 Papers
 
 > Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences.
 > *Bioinformatics*, **34**:3094-3100. [doi:10.1093/bioinformatics/bty191][doi]
@@ -180,6 +178,11 @@ and/or:
 > *Bioinformatics*, **37**:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2]
 
 # Changelog
+### 0.1.21 minimap2 2.28
+#### Breaking Changes
++ Map now returns Arc String's to reduce memory allocation for large and/or repetitive jobs
++ map now takes an additional argument, query_name: Option<impl AsRef<[u8]>>
+
 ### 0.1.20 minimap2 2.28
 + Fix htslib errors. No update to -sys crate needed.
 

src/lib.rs

@@ -1,4 +1,4 @@
-//! API providing a rusty interface to minimap2 or mm2-fast libraries.
+//! API providing a rusty interface to minimap2
 //!
 //! This library supports statically linking and compiling minimap2 directly, no separate install is required.
 //!
@@ -12,10 +12,26 @@
 //! # Crate Features
 //! This crate has multiple create features available.
 //! * map-file - Enables the ability to map a file directly to a reference. Enabled by deafult
-//! * mm2-fast - Uses the mm2-fast library instead of standard minimap2
 //! * htslib - Provides an interface to minimap2 that returns rust_htslib::Records
 //! * simde - Enables SIMD Everywhere library in minimap2
-//! * sse - Enables the use of SSE instructions
+//! * zlib-ng - Enables the use of zlib-ng for faster compression
+//! * curl - Enables curl for htslib
+//! * static - Builds minimap2 as a static library
+//! * sse2only - Builds minimap2 with only SSE2 support
+//! 
+//! ## Previously Supported Features
+//! * mm2-fast - Uses the mm2-fast library instead of standard minimap2
+//! 
+//! If needed, this can be re-enabled.
+//! 
+//! # Compile-time options
+//! I recommend the following:
+//! ```toml
+//! [profile.release]
+//! opt-level = 3
+//! lto = "fat"
+//! codegen-units  = 1
+//! ```
 //!
 //! # Examples
 //! ## Mapping a file to a reference
@@ -2050,7 +2066,19 @@ mod tests {
 
             jh1.join().unwrap();
         });
+    }
 
+    // Test aligner cloning for flag permanence
+    #[test]
+    fn aligner_cloning_flags() {
+        let aligner = Aligner::builder().map_ont().with_cigar().with_index("yeast_ref.mmi", None).unwrap();
+        // Confirm with_cigar is set
+        // self.mapopt.flag |= MM_F_CIGAR as i64;
+        assert_eq!(aligner.mapopt.flag & MM_F_CIGAR as i64, MM_F_CIGAR as i64);
 
+        // Clone aligner
+        let aligner_clone = aligner.clone();
+        assert_eq!(aligner_clone.mapopt.flag & MM_F_CIGAR as i64, MM_F_CIGAR as i64);
     }
+
 }