56 breaking releases
new 0.57.0 | Apr 22, 2024 |
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0.55.0 | Mar 28, 2024 |
0.49.0 | Dec 14, 2023 |
0.48.0 | Nov 14, 2023 |
0.2.0 | Jul 30, 2021 |
#1278 in Parser implementations
2,075 downloads per month
Used in 34 crates
(9 directly)
760KB
18K
SLoC
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 = sam::io::reader::Builder::default().build_from_path("sample.sam")?;
let header = reader.read_header()?;
for result in reader.records() {
let record = result?;
// ...
}
Dependencies
~2.8–5MB
~81K SLoC