Crate rust_htslib [] [src]

Rust-HTSlib provides a high level BAM API. 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
bcf
htslib
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
utils