Struct IndexedBcfReader 

pub struct IndexedBcfReader { /* private fields */ }

IndexedBcfReader allows random access to a specific genome interval of the BCF file using a CSI index file. It is an wrapper around ParMultiGzipReader<BufReader<File>> to allow parallelizable bgzip decompression.

The source should be BCF file consisting of small BGZF blocks.

Example

use bcf_reader::*;
// create indexed bcf reader
let mut reader =
    IndexedBcfReader::from_path("testdata/test3.bcf", "testdata/test3.bcf.csi", None).unwrap();
// read though header
let _header = reader.read_header();
// define targeted genome interval
let interval = GenomeInterval {
    chrom_id: 0,
    start: 1489230 - 1,
    end: Some(1498509 - 1),
};
// set interval
reader.set_interval(interval);
// create a reusable record
let mut record = Record::default();

let mut pos_found = vec![];
// iterate records from the targeted genome interval
while let Ok(_) = reader.read_record(&mut record) {
    pos_found.push(record.pos() + 1);
}

assert_eq!(
    pos_found,
    vec![
        1489230, 1489979, 1490069, 1490311, 1492233, 1492337, 1493505, 1494178, 1495207,
        1495403, 1495746, 1496047, 1497964, 1498188,
    ]
)

Implementations

impl IndexedBcfReader

pub fn from_path( path_bcf: impl AsRef<Path>, path_csi: impl AsRef<Path>, max_gzip: Option<usize>, ) -> Result<Self>

Create an IndexedBcfReader from paths to a bcf file and a corresponding csi index file.

• max_gzip, the number of gzip blocks to read before each batch parallelized decompression. See ParMultiGzipReader::from_reader (by default (None) use 3); this construct will automaticall read and parse the header

pub fn read_header(&mut self) -> Result<Header>

Read the header bytes, parse them and return a Header

pub fn set_interval(&mut self, genome_interval: GenomeInterval) -> Result<()>

Jump the file pointer to the begining to the targeted genome interval

If no site within the genome interval, read_record will return Err(_)

pub fn read_record(&mut self, record: &mut Record) -> Result<()>

Read one record. Should be called after header is parsed.

If set_interval has been called, only records within the given interval will be read.