Struct BatchedSamReader 

pub struct BatchedSamReader<R: Read> { /* private fields */ }

Adaptive buffered reader for SAM input from bwa mem.

Reads bytes into a growable buffer, tracks batch boundaries like bwa, and grows the buffer based on observed batch sizes. Never shrinks.

Implementations

impl<R: Read> BatchedSamReader<R>

pub fn new(reader: R, chunk_size: u64) -> Self

Create a new reader with the given bwa chunk size (-K value).

pub fn fill_buffer(&mut self) -> Result<bool>

Fill buffer by reading chunks until buffer is full or EOF.

Handles edge cases:

• Grows buffer proactively if unparsed data > 50% of capacity
• Preserves partial records at end of buffer
• Never loses data

Errors

Returns an error if the underlying reader fails.

pub fn buffer(&self) -> &[u8]

Get current buffer slice for parsing.

pub fn record_parsed(&mut self, seq_len: usize, bytes_consumed: usize) -> bool

Called after parsing a SAM record.

Tracks bases and records for batch detection. When a batch boundary is reached, may grow the buffer based on observed batch size.

Returns true if the buffer was grown.

pub fn advance(&mut self, bytes: usize)

Advance parse position without tracking as a record (e.g., for headers).

pub fn capacity(&self) -> usize

Get current buffer capacity.

pub fn batches_completed(&self) -> usize

Get number of completed batches.

pub fn total_bytes_read(&self) -> usize

Get total bytes read from input.

pub fn chunk_size(&self) -> u64

Get the configured chunk size (bwa -K value).

Trait Implementations

impl<R: Read> BufRead for BatchedSamReader<R>

Implement BufRead trait for use with SAM readers (e.g., noodles).

When used via BufRead, batch tracking is not active since we don’t have visibility into SAM record boundaries. The buffer still grows proactively based on fill ratio, similar to GrowableReader.

fn fill_buf(&mut self) -> Result<&[u8]>

Returns the contents of the internal buffer, filling it with more data, via Read methods, if empty.

fn consume(&mut self, amt: usize)

Marks the given amount of additional bytes from the internal buffer as having been read. Subsequent calls to read only return bytes that have not been marked as read.

fn has_data_left(&mut self) -> Result<bool, Error>

🔬This is a nightly-only experimental API. (buf_read_has_data_left)

Checks if there is any data left to be read.

fn read_until(&mut self, byte: u8, buf: &mut Vec<u8>) -> Result<usize, Error>

Reads all bytes into buf until the delimiter byte or EOF is reached.

fn skip_until(&mut self, byte: u8) -> Result<usize, Error>

Skips all bytes until the delimiter byte or EOF is reached.

fn read_line(&mut self, buf: &mut String) -> Result<usize, Error>

Reads all bytes until a newline (the 0xA byte) is reached, and append them to the provided String buffer.

fn split(self, byte: u8) -> Split<Self>

where Self: Sized,

Returns an iterator over the contents of this reader split on the byte byte.

fn lines(self) -> Lines<Self>

where Self: Sized,

Returns an iterator over the lines of this reader.

impl<R: Read> Read for BatchedSamReader<R>

Implement Read trait for compatibility with standard I/O.

fn read(&mut self, buf: &mut [u8]) -> Result<usize>

Pull some bytes from this source into the specified buffer, returning how many bytes were read.

fn read_vectored(&mut self, bufs: &mut [IoSliceMut<'_>]) -> Result<usize, Error>

Like read, except that it reads into a slice of buffers.

fn is_read_vectored(&self) -> bool

🔬This is a nightly-only experimental API. (can_vector)

Determines if this Reader has an efficient read_vectored implementation.

fn read_to_end(&mut self, buf: &mut Vec<u8>) -> Result<usize, Error>

Reads all bytes until EOF in this source, placing them into buf.

fn read_to_string(&mut self, buf: &mut String) -> Result<usize, Error>

Reads all bytes until EOF in this source, appending them to buf.

fn read_exact(&mut self, buf: &mut [u8]) -> Result<(), Error>

Reads the exact number of bytes required to fill buf.

fn read_buf(&mut self, buf: BorrowedCursor<'_>) -> Result<(), Error>

🔬This is a nightly-only experimental API. (read_buf)

Pull some bytes from this source into the specified buffer.

fn read_buf_exact(&mut self, cursor: BorrowedCursor<'_>) -> Result<(), Error>

🔬This is a nightly-only experimental API. (read_buf)

Reads the exact number of bytes required to fill cursor.

fn by_ref(&mut self) -> &mut Self

where Self: Sized,

Creates a “by reference” adapter for this instance of Read.

fn bytes(self) -> Bytes<Self>

where Self: Sized,

Transforms this Read instance to an Iterator over its bytes.

fn chain<R>(self, next: R) -> Chain<Self, R>

where R: Read, Self: Sized,

Creates an adapter which will chain this stream with another.

fn take(self, limit: u64) -> Take<Self>

where Self: Sized,

Creates an adapter which will read at most limit bytes from it.

fn read_array<const N: usize>(&mut self) -> Result<[u8; N], Error>

where Self: Sized,

🔬This is a nightly-only experimental API. (read_array)

Read and return a fixed array of bytes from this source.