noodles_bgzf/gzi/
index.rs

1use std::io;
2
3use crate::VirtualPosition;
4
5/// A gzip index (GZI).
6///
7/// A gzip index holds compressed-uncompressed position pairs.
8///
9/// Like the physical index, this does _not_ include the position of the first block, which is
10/// implicitly at 0.
11#[derive(Clone, Debug, Default, Eq, PartialEq)]
12pub struct Index(Vec<(u64, u64)>);
13
14impl Index {
15    /// Returns the virtual position at the given uncompressed position.
16    ///
17    /// # Examples
18    ///
19    /// ```
20    /// use noodles_bgzf::{self as bgzf, gzi};
21    ///
22    /// let index = gzi::Index::default();
23    /// assert_eq!(index.query(0)?, bgzf::VirtualPosition::default());
24    ///
25    /// let index = gzi::Index::from(vec![(8, 21), (13, 55)]);
26    /// assert_eq!(index.query(0)?, bgzf::VirtualPosition::default());
27    /// assert_eq!(index.query(13)?, bgzf::VirtualPosition::try_from((0, 13))?);
28    /// assert_eq!(index.query(34)?, bgzf::VirtualPosition::try_from((8, 13))?);
29    /// assert_eq!(index.query(89)?, bgzf::VirtualPosition::try_from((13, 34))?);
30    /// Ok::<_, Box<dyn std::error::Error>>(())
31    /// ```
32    pub fn query(&self, pos: u64) -> io::Result<VirtualPosition> {
33        let i = self.0.partition_point(|r| r.1 <= pos);
34
35        let (compressed_pos, uncompressed_pos) = if i == 0 { (0, 0) } else { self.0[i - 1] };
36
37        let block_data_pos = u16::try_from(pos - uncompressed_pos)
38            .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;
39
40        VirtualPosition::try_from((compressed_pos, block_data_pos))
41            .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
42    }
43}
44
45impl AsRef<[(u64, u64)]> for Index {
46    fn as_ref(&self) -> &[(u64, u64)] {
47        &self.0
48    }
49}
50
51impl From<Vec<(u64, u64)>> for Index {
52    fn from(index: Vec<(u64, u64)>) -> Self {
53        Self(index)
54    }
55}
noodles_bgzf/gzi/index.rs

noodles_bgzf/gzi/
index.rs
