1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82

use std::{
    ffi::{OsStr, OsString},
    fs::File,
    io,
    path::{Path, PathBuf},
};

use noodles_bgzf as bgzf;
use noodles_csi::io::IndexedReader;

use crate::Index;

/// An indexed reader builder.
#[derive(Default)]
pub struct Builder {
    index: Option<Index>,
}

impl Builder {
    /// Sets an index.
    pub fn set_index(mut self, index: Index) -> Self {
        self.index = Some(index);
        self
    }

    /// Builds an indexed reader from a path.
    pub fn build_from_path<P>(self, src: P) -> io::Result<IndexedReader<bgzf::Reader<File>, Index>>
    where
        P: AsRef<Path>,
    {
        let src = src.as_ref();

        let index = match self.index {
            Some(index) => index,
            None => read_associated_index(src)?,
        };

        let file = File::open(src)?;

        Ok(IndexedReader::new(file, index))
    }
}

fn read_associated_index<P>(src: P) -> io::Result<Index>
where
    P: AsRef<Path>,
{
    crate::read(build_index_src(src, "tbi"))
}

fn build_index_src<P, S>(src: P, ext: S) -> PathBuf
where
    P: AsRef<Path>,
    S: AsRef<OsStr>,
{
    push_ext(src.as_ref().into(), ext)
}

fn push_ext<S>(path: PathBuf, ext: S) -> PathBuf
where
    S: AsRef<OsStr>,
{
    let mut s = OsString::from(path);
    s.push(".");
    s.push(ext);
    PathBuf::from(s)
}

#[cfg(test)]
mod tests {
    use std::path::PathBuf;

    use super::*;

    #[test]
    fn test_push_ext() {
        assert_eq!(
            push_ext(PathBuf::from("annotations.gff.gz"), "tbi"),
            PathBuf::from("annotations.gff.gz.tbi")
        );
    }
}