Struct noodles_gtf::Reader

pub struct Reader<R> { /* private fields */ }

A GTF reader.

Implementations

impl<R> Reader<R>

where R: BufRead,

pub fn new(inner: R) -> Self

Creates a GTF reader.

Examples

use noodles_gtf as gtf;
let data = [];
let reader = gtf::Reader::new(&data[..]);

pub fn read_line(&mut self, buf: &mut String) -> Result<usize>

Reads a raw GTF line.

Examples

use noodles_gtf as gtf;

let data = b"sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id \"ndls0\"; transcript_id \"ndls0\";";
let mut reader = gtf::Reader::new(&data[..]);

let mut buf = String::new();
reader.read_line(&mut buf)?;

assert_eq!(
    buf,
    "sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id \"ndls0\"; transcript_id \"ndls0\";"
);

pub fn lines(&mut self) -> impl Iterator<Item = Result<Line>> + '_

Returns an iterator over lines starting from the current stream position.

Examples

use noodles_gtf as gtf;

let data = b"##format: gtf
sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id \"g0\"; transcript_id \"t0\";
";
let mut reader = gtf::Reader::new(&data[..]);

let mut lines = reader.lines();

let line = lines.next().transpose()?;
assert_eq!(line, Some(gtf::Line::Comment(String::from("#format: gtf"))));

let line = lines.next().transpose()?;
assert!(matches!(line, Some(gtf::Line::Record(_))));

assert!(lines.next().is_none());

pub fn records(&mut self) -> impl Iterator<Item = Result<Record>> + '_

Returns an iterator over records starting from the current stream position.

Examples

use noodles_core::Position;
use noodles_gtf as gtf;

let data = b"##format: gtf
sq0\tNOODLES\tgene\t8\t13\t.\t+\t.\tgene_id \"g0\"; transcript_id \"t0\";
";
let mut reader = gtf::Reader::new(&data[..]);

let mut records = reader.records();

let record = records.next().transpose()?;
assert_eq!(record.map(|r| r.start()), Position::new(8));
// ...

assert!(records.next().is_none());

Examples found in repository

examples/gtf_view.rs (line 18)

fn main() -> io::Result<()> {
    let src = env::args().nth(1).expect("missing src");

    let mut reader = File::open(src).map(BufReader::new).map(gtf::Reader::new)?;

    for result in reader.records() {
        let record = result?;
        println!("{record}");
    }

    Ok(())
}

examples/gtf_count.rs (line 19)

fn main() -> io::Result<()> {
    let src = env::args().nth(1).expect("missing src");

    let mut reader = File::open(src).map(BufReader::new).map(gtf::Reader::new)?;
    let mut n = 0;

    for result in reader.records() {
        let _ = result?;
        n += 1;
    }

    println!("{n}");

    Ok(())
}

impl<R> Reader<Reader<R>>

where R: Read + Seek,

pub fn query<'r, I>( &'r mut self, index: &I, region: &'r Region ) -> Result<impl Iterator<Item = Result<Record>> + 'r>

where I: BinningIndex,

Returns an iterator over records that intersects the given region.