Struct bam::bgzip::Block

pub struct Block { /* fields omitted */ }

A bgzip block, that can contain compressed, uncompressed data, or both.

You can extend uncompressed data using extend_contents, and and then compress the block using compress.

Implementations

impl Block

pub fn new() -> Self

Creates an empty block.

pub fn reset(&mut self)

Resets a block (clears both compressed and uncompressed data).

pub fn reset_compression(&mut self)

Resets compressed data, if present. This function is needed if you want to update uncompressed contents.

pub fn make_empty(&mut self)

Makes a block a compressed block with empty contents. It is different from reset as the block will have valid compressed data and can be written.

pub fn extend_contents(&mut self, buf: &[u8]) -> usize

Extends uncompressed contents and returns the number of consumed bytes. The only case when the number of consumed bytes is less then the size of the buf is when the content size reaches maximum size MAX_BLOCK_SIZE. However, it is not recommended to fill the contents completely to MAX_BLOCK_SIZE as the compressed size may become too big (bigger than MAX_COMPRESSED_SIZE).

This function panics if the block contains compressed data (see reset_compression).

pub fn uncompressed_size(&self) -> u32

Returns the size of the uncompressed data (this works even if the block was not decompressed).

pub fn compressed_size(&self) -> u32

Returns the size of the compressed data. If the block was not compressed, the function returns zero. Note, that the compressed size does not include header and footer of the bgzip block.

pub fn block_size(&self) -> Option<u32>

Returns the size of the block (sum size of compressed data, header and footer). Returns None if the block was not compressed yet.

pub fn offset(&self) -> Option<u64>

Returns a block offset, if present.

pub fn state(&self) -> BlockState

Returns the state of the block.

pub fn compress(&mut self, compression: Compression) -> Result<()>

Compresses block contents. Note that if the contents are empty, the function will compress them into a valid block (see make_empty).

If the compressed size is bigger than MAX_COMPRESSED_SIZE, the function returns WriteZero. Function panics if the block is already compressed.

pub fn dump<W: Write>(&self, stream: &mut W) -> Result<()>

Writes the compressed block to stream. The function panics if the block was not compressed.

pub fn load<R: Read>(
    &mut self,
    offset: Option<u64>,
    stream: &mut R
) -> Result<(), BlockError>

Reads the compressed contents from stream. Panics if the block is non-empty (consider using reset).

pub fn decompress(&mut self) -> Result<(), BlockError>

Decompresses block contents. This function panics if the block was already decompressed or if the block is empty.

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

Access uncompressed data.

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

Access compressed data (without header and footer). Panics if the block is not compressed.

pub fn crc32(&self) -> u32

Returns CRC32 hash of the uncompressed data. Panics if the block is not compressed.

pub fn split_contents(
    &mut self,
    first_size: usize,
    second_part: &mut [u8]
) -> usize

Truncates uncompressed contents on first_size, writes the remaining data into second_part, and returns the number of bytes written into second_part.

Panics, if the second_part is not big enough.

pub fn split_into_two(&mut self) -> Block

The function trims the contents of self, and returns the second half in a new Block. The function panics if the initial block was compressed or its uncompressed size is less than 2 bytes.

Trait Implementations

impl Clone for Block

fn clone(&self) -> Block

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.