69 breaking releases
new 0.70.0 | Nov 7, 2024 |
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0.2.1 | Jul 30, 2021 |
#125 in Science
4,024 downloads per month
Used in 42 crates
(6 directly)
1MB
26K
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, ®ion)?;
for result in query {
let record = result?;
// ...
}
Dependencies
~2.8–9MB
~80K SLoC