Crate extended_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, let’s say that we use samtools to view the header of a test file:

samtools view -H test/test.bam
@SQ    SN:CHROMOSOME_I    LN:15072423
@SQ    SN:CHROMOSOME_II    LN:15279345
@SQ    SN:CHROMOSOME_III    LN:13783700
@SQ    SN:CHROMOSOME_IV    LN:17493793
@SQ    SN:CHROMOSOME_V    LN:20924149

We can reproduce that with Rust-Htslib. Reading BAM files and printing the header to the screen is as easy as

use extended_htslib::{bam, bam::Read};


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

// print header records to the terminal, akin to samtool
for (key, records) in header.to_hashmap() {
    for record in records {
         println!("@{}\tSN:{}\tLN:{}", key, record["SN"], record["LN"]);
    }
}

which results in the following output, equivalent to samtools.

@SQ    SN:CHROMOSOME_I    LN:15072423
@SQ    SN:CHROMOSOME_II    LN:15279345
@SQ    SN:CHROMOSOME_III    LN:13783700
@SQ    SN:CHROMOSOME_IV    LN:17493793
@SQ    SN:CHROMOSOME_V    LN:20924149

We can also read directly from the BAM file and write to an output file

use extended_htslib::{bam, bam::Read};

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, bam::Format::Bam).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 (requires a RegionString region):

use extended_htslib::{bam::{self,pileup}, bam::Read};

let mut path = "test/test.bam";

let config = pileup::RustPileupConfig::default();
let pos = bam::FetchDefinition::RegionString("CHROMOSOME_I".as_bytes(), 1, 100);
let config = pileup::RustPileupConfig::default();
let mut po = pileup::RustPileups::new(path, None, None, None, pos, config).unwrap();
for pileup in po {
    println!("Pileup is {}", pileup.to_string());
    println!("Base is {}",pileup.getbase());
}

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

use extended_htslib::{bam, bam::Read};

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

bam.fetch(("CHROMOSOME_I", 0, 20)).unwrap();
// afterwards, read or pileup in this region

See

• fetch
• records
• read
• pileup

Modules

bam

Module for working with SAM, BAM, and CRAM files.

bcf

Module for working with VCF and BCF files.

bgzf

Module for working with bgzipped file.

errors

faidx

Module for working with faidx-indexed FASTA files.

htslib

Re-export hts-sys htslib bindings

tbx

Module for working with tabix-indexed text files.

tpool

utils

Module with utility code.