Struct bam::bgzip::read::SeekReader [−][src]
Expand description
A bgzip reader, that allows to jump between blocks.
You can open the reader using from_path or
from_stream.
Additional threads are used to decompress blocks, while the
main thread reads the blocks from a file/stream. If additional_threads is 0, the main thread
will decompress blocks itself.
When this reader is opened, it does read not anything, until you specify reading regions.
You can do that by using Seek trait, but it is recommended to use methods
set_chunks, make_consecutive and
from_offset. Note, that in multi-threaded SeekReader it is important to
correctly set future reading queue (use set_chunks instead of running from_offset multiple times).
You can read the contents using io::Read,
or read blocks using ReadBgzip trait.
Implementations
Opens a reader from a stream.
Sets the current chunks. Each chunk specifies a region of
the bgzip file. The multi-thread reader reads and decompresses blocks from the chunks
in advance (but does not immediately read all blocks).
This function resets the current reading queue (from the previous set_chunks or
make_consecutive calls).
chunks must be sorted and should not intersect each other.
Sets the reader in a consecutive mode starting with offset 0, and continuing until the end of the stream.
This function resets the current reading queue.
Sets the reader in a consecutive mode starting with offset, and continuing until the end of the stream.
This function resets the current reading queue.
Consumes the reader and returns inner stream.
Returns current virtual offset.
If the reader has not started, returns the start of the first chunk. If the reader finished the current queue, returns the end of the last chunk.
Trait Implementations
Pull some bytes from this source into the specified buffer, returning how many bytes were read. Read more
Like read, except that it reads into a slice of buffers. Read more
can_vector)Determines if this Reader has an efficient read_vectored
implementation. Read more
Read all bytes until EOF in this source, placing them into buf. Read more
Read all bytes until EOF in this source, appending them to buf. Read more
Read the exact number of bytes required to fill buf. Read more
read_buf)Pull some bytes from this source into the specified buffer. Read more
read_buf)Read the exact number of bytes required to fill buf. Read more
Creates a “by reference” adaptor for this instance of Read. Read more
Creates an adapter which will chain this stream with another. Read more
Reads the next block in a queue. Note, that if the chunks vector contain the same block
twice, it will be read only once.
Returns the current block, if possible. This function does not advance the stream.
Seek to a block with a given block offset, and return new block offset.
This function is not implemented for SeekFrom::End because it will increase running time and
is rarely needed.
If the offset is positive, but incorrect (out of bounds or does not point to a start of a block), this function
will return Ok, but consecutive read run will return an error.
Note: consider running functions from_offset,
make_consecutive or set_chunks, as they are more explicit.
Additionally, set_chunks works faster in a multi-threaded reader.
seek_stream_len)Returns the length of this stream (in bytes). Read more
Auto Trait Implementations
impl<R> !RefUnwindSafe for SeekReader<R>
impl<R> Send for SeekReader<R> where
R: Send,
impl<R> !Sync for SeekReader<R>
impl<R> Unpin for SeekReader<R> where
R: Unpin,
impl<R> !UnwindSafe for SeekReader<R>
Blanket Implementations
Mutably borrows from an owned value. Read more
Reads an unsigned 8 bit integer from the underlying reader. Read more
Reads a signed 8 bit integer from the underlying reader. Read more
Reads an unsigned 16 bit integer from the underlying reader. Read more
Reads a signed 16 bit integer from the underlying reader. Read more
Reads an unsigned 24 bit integer from the underlying reader. Read more
Reads a signed 24 bit integer from the underlying reader. Read more
Reads an unsigned 32 bit integer from the underlying reader. Read more
Reads a signed 32 bit integer from the underlying reader. Read more
Reads an unsigned 48 bit integer from the underlying reader. Read more
Reads a signed 48 bit integer from the underlying reader. Read more
Reads an unsigned 64 bit integer from the underlying reader. Read more
Reads a signed 64 bit integer from the underlying reader. Read more
Reads an unsigned 128 bit integer from the underlying reader. Read more
Reads a signed 128 bit integer from the underlying reader. Read more
Reads an unsigned n-bytes integer from the underlying reader. Read more
Reads a signed n-bytes integer from the underlying reader. Read more
Reads an unsigned n-bytes integer from the underlying reader.
Reads a signed n-bytes integer from the underlying reader.
Reads a IEEE754 single-precision (4 bytes) floating point number from the underlying reader. Read more
Reads a IEEE754 double-precision (8 bytes) floating point number from the underlying reader. Read more
Reads a sequence of unsigned 16 bit integers from the underlying reader. Read more
Reads a sequence of unsigned 32 bit integers from the underlying reader. Read more
Reads a sequence of unsigned 64 bit integers from the underlying reader. Read more
Reads a sequence of unsigned 128 bit integers from the underlying reader. Read more
Reads a sequence of signed 8 bit integers from the underlying reader. Read more
Reads a sequence of signed 16 bit integers from the underlying reader. Read more
Reads a sequence of signed 32 bit integers from the underlying reader. Read more
Reads a sequence of signed 64 bit integers from the underlying reader. Read more
Reads a sequence of signed 128 bit integers from the underlying reader. Read more
Reads a sequence of IEEE754 single-precision (4 bytes) floating point numbers from the underlying reader. Read more
Reads a sequence of IEEE754 double-precision (8 bytes) floating point numbers from the underlying reader. Read more