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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;
#[derive(Default)]
pub struct Builder {
index: Option<csi::Index>,
}
impl Builder {
pub fn set_index(mut self, index: csi::Index) -> Self {
self.index = Some(index);
self
}
pub fn build_from_path<P>(mut self, src: P) -> io::Result<IndexedReader<File>>
where
P: AsRef<Path>,
{
let src = src.as_ref();
if self.index.is_none() {
let index_src = build_index_src(src);
self.index = tabix::read(index_src).map(Some)?;
}
let file = File::open(src)?;
self.build_from_reader(file)
}
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 build_index_src<P>(src: P) -> PathBuf
where
P: AsRef<Path>,
{
const EXT: &str = "tbi";
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_build_index_src() {
assert_eq!(
build_index_src("sample.vcf.gz"),
PathBuf::from("sample.vcf.gz.tbi")
);
}
}