Crate noodles_sam

Expand description

noodles-sam handles the reading and writing of the SAM (Sequence Alignment/Map) format.

SAM is a format typically used to store biological sequences, either mapped to a reference sequence or unmapped. It has two sections: a header and a list of records.

The header mostly holds meta information about the data: a header describing the file format version, reference sequences reads map to, read groups reads belong to, programs that previously manipulated the data, and free-form comments. The header is optional and may be empty.

Each record represents a read, a linear alignment of a segment. Records have fields describing how a read was mapped (or not) to a reference sequence.

Examples

Read all records from a file

use noodles_sam as sam;

let mut reader = File::open("sample.sam")
    .map(BufReader::new)
    .map(sam::Reader::new)?;

let header = reader.read_header()?.parse()?;

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