Crate minimap2 

API providing a rusty interface to minimap2

This library supports statically linking and compiling minimap2 directly, no separate install is required.

Implementation

This is a wrapper library around minimap2-sys, which are lower level bindings for minimap2.

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
• 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

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:

[profile.release]
opt-level = 3
lto = "fat"
codegen-units  = 1

Examples

Mapping a file to a reference

use minimap2::{Aligner, Preset};
let mut aligner = Aligner::builder()
.map_ont()
.with_index_threads(8)
.with_cigar()
.with_index("ReferenceFile.fasta", None)
.expect("Unable to build index");

let seq = b"ACTGACTCACATCGACTACGACTACTAGACACTAGACTATCGACTACTGACATCGA";
let alignment = aligner
.map(seq, false, false, None, None, Some(b"Sample Query"))
.expect("Unable to align");

Mapping a file to an individual target sequence

use minimap2::{Aligner, Preset};
let aligner = Aligner::builder().map_ont().with_seq(seq.as_bytes()).expect("Unable to build index");
let query = b"CGGCACCAGGTTAAAATCTGAGTGCTGCAATAGGCGATTACAGTACAGCACCCAGCCTCCG";
let hits = aligner.map(query, false, false, None, None, Some(b"Query Name"));
assert_eq!(hits.unwrap().len(), 1);

Re-exports

pub use minimap2_sys as ffi;

Modules

htslib

Provides an interface to minimap2 that returns rust_htslib::Records

Structs

Aligner

Aligner struct, mimicking minimap2’s python interface

Alignment

Alignment struct when alignment flag is set

Built

Junction

Represents a splice junction and its associated score

Mapping

Mapping result

PresetSet

Unset

Enums

AlignmentType

Alignment type

FileFormat

Preset

Preset’s for minimap2 config

Strand

Strand enum

Traits

AcceptsParams

BuilderState

Type Aliases

IdxOpt

Alias for mm_idxopt_t

MapOpt

Alias for mm_mapop_t