noodles_fasta/io/
indexed_reader.rs

1//! Indexed FASTA reader.
2
3mod builder;
4
5pub use self::builder::Builder;
6
7use std::io::{self, BufRead, Seek};
8
9use noodles_core::Region;
10
11use super::Reader;
12use crate::{fai, Record};
13
14/// An indexed FASTA reader.
15pub struct IndexedReader<R> {
16    inner: Reader<R>,
17    index: fai::Index,
18}
19
20impl<R> IndexedReader<R>
21where
22    R: BufRead,
23{
24    /// Creates a new indexed FASTA reader.
25    pub fn new(inner: R, index: fai::Index) -> Self {
26        Self {
27            inner: Reader::new(inner),
28            index,
29        }
30    }
31
32    /// Returns a reference to the underlying reader.
33    pub fn get_ref(&self) -> &R {
34        self.inner.get_ref()
35    }
36
37    /// Returns a mutable reference to the underlying reader.
38    pub fn get_mut(&mut self) -> &mut R {
39        self.inner.get_mut()
40    }
41
42    /// Returns the underlying reader.
43    pub fn into_inner(self) -> R {
44        self.inner.into_inner()
45    }
46
47    /// Reads a raw definition line.
48    pub fn read_definition(&mut self, buf: &mut String) -> io::Result<usize> {
49        self.inner.read_definition(buf)
50    }
51
52    /// Reads a sequence.
53    pub fn read_sequence(&mut self, buf: &mut Vec<u8>) -> io::Result<usize> {
54        self.inner.read_sequence(buf)
55    }
56
57    /// Returns the associated index.
58    pub fn index(&self) -> &fai::Index {
59        &self.index
60    }
61}
62
63impl<R> IndexedReader<R>
64where
65    R: BufRead + Seek,
66{
67    /// Returns a record of the given region.
68    pub fn query(&mut self, region: &Region) -> io::Result<Record> {
69        self.inner.query(&self.index, region)
70    }
71}
noodles_fasta/io/indexed_reader.rs

noodles_fasta/io/
indexed_reader.rs
