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
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130

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

use noodles_csi as csi;
use noodles_tabix as tabix;

use super::IndexedReader;

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

impl Builder {
    /// Sets an index.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_csi as csi;
    /// use noodles_vcf::indexed_reader::Builder;
    ///
    /// let index = csi::Index::default();
    /// let builder = Builder::default().set_index(index);
    /// ```
    pub fn set_index(mut self, index: csi::Index) -> Self {
        self.index = Some(index);
        self
    }

    /// Builds an indexed VCF reader from a path.
    ///
    /// # Examples
    ///
    /// ```no_run
    /// use noodles_vcf::indexed_reader::Builder;
    /// let reader = Builder::default().build_from_path("sample.vcf.gz")?;
    /// # Ok::<_, std::io::Error>(())
    /// ```
    pub fn build_from_path<P>(self, src: P) -> io::Result<IndexedReader<File>>
    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))
    }

    /// Builds an indexed VCF reader from a reader.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_csi as csi;
    /// use noodles_vcf::indexed_reader::Builder;
    ///
    /// let index = csi::Index::default();
    /// let reader = Builder::default()
    ///     .set_index(index)
    ///     .build_from_reader(io::empty())?;
    /// # Ok::<_, io::Error>(())
    /// ```
    pub fn build_from_reader<R>(self, reader: R) -> io::Result<IndexedReader<R>>
    where
        R: Read,
    {
        let index = self
            .index
            .ok_or_else(|| io::Error::new(io::ErrorKind::InvalidInput, "missing index"))?;

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

fn read_associated_index<P>(src: P) -> io::Result<csi::Index>
where
    P: AsRef<Path>,
{
    let src = src.as_ref();

    match tabix::read(build_index_src(src, "tbi")) {
        Ok(index) => Ok(index),
        Err(e) if e.kind() == io::ErrorKind::NotFound => csi::read(build_index_src(src, "csi")),
        Err(e) => Err(e),
    }
}

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 super::*;

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