[−][src]Module bam::bgzip

Bgzip files (BGZF) and bgzip blocks.

This modules contains several readers and writers of Bgzip files:

Readers

Consecutive Reader - reads bgzip file consecutively.
Seek Reader - seeks and reads bgzip blocks given an offset.
Chunks Reader - wrapper around the Seek Reader, that reads multiple blocks given a vector of chunks.

Writer - writes whole bgzip blocks.
Sentence Writer - wrapper around the Writer, that implements the Write trait. In addition, it allows to end sentences - marks points, in which it is preferable to break the stream and start a new bgzip block. For example, each BAM record represents a separate sentence, and SentenceWriter will try not to split a record between two blocks.

Block	Bgzip block. Both uncompressed and compressed size should not be bigger than `MAX_BLOCK_SIZE = 65536`.
ChunksReader	Reader of Bgzip blocks given for a vector of chunks. Wrapper of SeekReader.
ConsecutiveReader	Consecutive reader of a bgzip file, it does not support random access, but also does not spend memory and time on caching.
SeekReader	Bgzip file reader, which allows to open bgzip blocks given an offset.
SeekReaderBuilder	Builder of bgzip file reader
SentenceWriter	A struct that allows to write bgzip files in sentences.
Writer	Bgzip writer, that allows to compress and write blocks with uncompressed size at most `MAX_BLOCK_SIZE = 65536`.

io::Error produced while reading a bgzip block.

Biggest possible compressed and uncompressed size