#bam #writer #record

noodles-bam

Binary Alignment/Map (BAM) format reader and writer

76 breaking releases

0.77.0 Mar 8, 2025
0.75.0 Jan 24, 2025
0.72.0 Dec 20, 2024
0.70.0 Nov 7, 2024
0.2.1 Jul 30, 2021

#12 in #bam

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3,589 downloads per month
Used in 46 crates (5 directly)

MIT license

1MB
28K SLoC

noodles-bam handles the reading and writing of the BAM (Binary Alignment/Map) file format.

The BAM format contains the same information as SAM (Sequence Alignment/Map), namely a SAM header and a list of records.

Examples

Read all records

use noodles_bam as bam;

let mut reader = bam::io::reader::Builder::default().build_from_path("sample.bam")?;
let header = reader.read_header()?;

for result in reader.records() {
    let record = result?;
    // ...
}

Query records

Querying allows filtering records by region. It requires an associated BAM index (BAI).

use noodles_bam as bam;

let mut reader = bam::io::indexed_reader::Builder::default().build_from_path("sample.bam")?;
let header = reader.read_header()?;

let region = "sq0:5-8".parse()?;
let query = reader.query(&header, &region)?;

for result in query {
    let record = result?;
    // ...
}

Dependencies

~3.5–10MB
~92K SLoC