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util/alignment/io/indexed_reader: Add examples
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zaeleus committed Jul 25, 2024
1 parent dde6d23 commit c3f5697
Showing 1 changed file with 49 additions and 0 deletions.
49 changes: 49 additions & 0 deletions noodles-util/src/alignment/io/indexed_reader.rs
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,18 @@ where
R: Read,
{
/// Reads the SAM header.
///
/// # Examples
///
/// ```no_run
/// use noodles_util::alignment;
///
/// let mut reader = alignment::io::indexed_reader::Builder::default()
/// .build_from_path("sample.bam")?;
///
/// let _header = reader.read_header()?;
/// # Ok::<_, std::io::Error>(())
/// ```
pub fn read_header(&mut self) -> io::Result<sam::Header> {
match self {
Self::Sam(reader) => reader.read_header(),
Expand All @@ -36,6 +48,23 @@ where
}

/// Returns an iterator over records starting from the current stream position.
///
/// # Examples
///
/// ```no_run
/// use noodles_util::alignment;
///
/// let mut reader = alignment::io::indexed_reader::Builder::default()
/// .build_from_path("sample.bam")?;
///
/// let header = reader.read_header()?;
///
/// for result in reader.records(&header) {
/// let record = result?;
/// // ...
/// }
/// # Ok::<_, std::io::Error>(())
/// ```
pub fn records<'r, 'h: 'r>(
&'r mut self,
header: &'h sam::Header,
Expand Down Expand Up @@ -71,6 +100,26 @@ where
R: Read + Seek,
{
/// Returns an iterator over records that intersects the given region.
///
/// # Examples
///
/// ```no_run
/// use noodles_util::alignment;
///
/// let mut reader = alignment::io::indexed_reader::Builder::default()
/// .build_from_path("sample.bam")?;
///
/// let header = reader.read_header()?;
///
/// let region = "sq0:8-13".parse()?;
/// let query = reader.query(&header, &region)?;
///
/// for result in query {
/// let record = result?;
/// // ...
/// }
/// # Ok::<_, Box<dyn std::error::Error>>(())
/// ```
pub fn query<'r, 'h: 'r>(
&'r mut self,
header: &'h sam::Header,
Expand Down

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