bam is a library that allows to read BAM files, written completely in Rust. Currently, it allows to only fetch reads from a region in an indexed bam file. In the future versions, non-indexed reader will be supported, as well as writing BAM files.
Having a library written completely in Rust reduces the number of dependencies and compilation time. Additionally, it removes the need to install additional C libraries.
Currently, there is only one available reader: bam::IndexedReader. The following code would
print SAM entries for all reads in a region:
``` extern crate bam;
fn main() { // If the index is not located at test.bam.bai, use // IndexedReader::frompathandindex(bampath, baipath) let mut reader = bam::IndexedReader::frompath("test.bam").unwrap();
// Need to clone header to have access to reference names as the
// reader will be blocked durint fetch.
let header = reader.header().clone();
for record in reader.fetch(1, 100_000, 200_000) {
let record = record.unwrap();
record.write_sam(&mut std::io::stdout(), &header).unwrap();
}
} ```
Additionally, you can use read_into(&mut record) to save time on record allocation:
let mut viewer = reader.fetch(1, 100_000, 200_000);
let mut record = bam::Record::new();
loop {
match viewer.read_into(&mut record) {
// New record is saved into record
Ok(()) => {},
// NoMoreRecords represents stop iteration
Err(bam::Error::NoMoreRecords) => break,
Err(e) => panic!("{}", e),
}
record.write_sam(&mut std::io::stdout(), &header).unwrap();
}
Each bgzip block contains a CRC32 checksum. By default, the bam crate does not compare
checksums to save time.
However, you can compare checksums by adding the following line to your Cargo.toml:
bam = { version = "*", features = ["check_crc"] }