bio2.bgzf

Undocumented in source.

Members

Aliases

BLOCK_SIZE
alias BLOCK_SIZE = BGZF_MAX_BLOCK_SIZE
Undocumented in source.
BlockBuffer
alias BlockBuffer = ubyte[BLOCK_SIZE]
Undocumented in source.
CRC32
alias CRC32 = immutable(uint)
Undocumented in source.
FilePos
alias FilePos = Nullable!ulong
Undocumented in source.

Classes

BgzfException
class BgzfException
Undocumented in source.

Functions

deflate
ubyte[] deflate(ubyte[] uncompressed_buf, ubyte[] compressed_buf, size_t uncompressed_size, CRC32 crc32)

Uncompress a zlib buffer (without header)

kick_off_reading_block_ahead
int kick_off_reading_block_ahead(ubyte[] uncompressed_buf, ubyte[] compressed_buf, size_t uncompressed_size, CRC32 crc32)
Undocumented in source. Be warned that the author may not have intended to support it.
read_blockx
Tuple!(size_t, FilePos) read_blockx(BgzfReader bgzf, FilePos fpos, ubyte[] uncompressed_buf)
Undocumented in source. Be warned that the author may not have intended to support it.

Properties

read_ubyte
ubyte read_ubyte [@property getter]
Undocumented in source. Be warned that the author may not have intended to support it.
read_uint
uint read_uint [@property getter]
Undocumented in source. Be warned that the author may not have intended to support it.
read_ushort
ushort read_ushort [@property getter]
Undocumented in source. Be warned that the author may not have intended to support it.

Structs

BgzfBlocks
struct BgzfBlocks

Simple block iterator

BgzfReader
struct BgzfReader

BgzfReader is designed to run on a single thread. All it does is fetch block headers and data, so the thread should easily keep up with IO. All data processing is happening lazily in other threads.

BgzfStream
struct BgzfStream

Streams bgzf data and fetch items by unit or buffer. These can go beyond the size of individual blocks(!)

BlockReadAhead
struct BlockReadAhead
BlockReadUnbuffered
struct BlockReadUnbuffered

Meta