Crate rust_htslib

Rust-Htslib provides a high level API to working with the common HTS file formats.

Htslib itself is the de facto standard implementation for reading and writing files for HTS alignments (SAM and BAM) as well as variant calls in VCF and BCF format.

For example, reading and writing BAM files is as easy as

use rust_htslib::bam;
use rust_htslib::prelude::*;

let mut bam = bam::Reader::from_path(&"test/test.bam").unwrap();
let header = bam::Header::from_template(bam.header());
let mut out = bam::Writer::from_path(&"test/out.bam", &header).unwrap();

// copy reverse reads to new BAM file
for r in bam.records() {
    let record = r.unwrap();
    if record.is_reverse() {
        out.write(&record).unwrap();
    }
}

Pileups can be performed with

use rust_htslib::bam;
use rust_htslib::prelude::*;

let mut bam = bam::Reader::from_path(&"test/test.bam").unwrap();

// pileup over all covered sites
for p in bam.pileup() {
    let pileup = p.unwrap();
    println!("{}:{} depth {}", pileup.tid(), pileup.pos(), pileup.depth());

    for alignment in pileup.alignments() {
        if !alignment.is_del() && !alignment.is_refskip() {
            println!("Base {}", alignment.record().seq()[alignment.qpos().unwrap()]);
        }
        // mark indel start
        match alignment.indel() {
            bam::pileup::Indel::Ins(len) => println!("Insertion of length {} between this and next position.", len),
            bam::pileup::Indel::Del(len) => println!("Deletion of length {} between this and next position.", len),
            bam::pileup::Indel::None => ()
        }
    }
}

In both cases, indexed BAM files can be seeked for specific regions, constraining either the record iterator or the pileups:

use rust_htslib::bam;
use rust_htslib::prelude::*;

let mut bam = bam::IndexedReader::from_path(&"test/test.bam").unwrap();

// seek to chr1:50000-100000
let tid = bam.header().tid(b"CHROMOSOME_I").unwrap();
bam.fetch(tid, 0, 20).unwrap();
// afterwards, read or pileup in this region

Modules

bam

Module for working with BAM files.

bcf

Module for working with VCF and BCF files.

htslib

This module exposes the raw Htslib bindings.

prelude

The purpose of this module is to provide reexports of core traits so that they can be then glob-imported all at once:

sam

Module for working with SAM files.

tbx

Module for working with tabix-indexed text files.

utils

Module with utility code.