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If you believe this is docs.rs' fault, open an issue.
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noodles-bam-0.62.0
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 std::{fs::File, io};
use noodles_bam as bam;
let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
reader.read_header()?;
reader.read_reference_sequences()?;
for result in reader.records() {
let record = result?;
println!("{:?}", record);
}
# Ok::<(), io::Error>(())
Query records
Querying allows filtering records by region. It requires an associated BAM index (BAI).
# use std::fs::File;
use noodles_bam::{self as bam, bai};
use noodles_core::Region;
use noodles_sam as sam;
let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
let header: sam::Header = reader.read_header()?.parse()?;
let reference_sequences = header.reference_sequences();
let index = bai::read("sample.bam.bai")?;
let region = Region::mapped("sq0", 17711..=28657);
let query = reader.query(&reference_sequences, &index, ®ion)?;
for result in query {
let record = result?;
println!("{:?}", record);
}
# Ok::<(), Box<dyn std::error::Error>>(())