compression.gdsn: Modify compression mode

In zhengxwen/gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files

Modify compression mode

Description

Modifie the compression mode of data field in the GDS node.

Usage

compression.gdsn(node,
    compress=c("", "ZIP", "ZIP_RA", "LZMA", "LZMA_RA", "LZ4", "LZ4_RA"))

Arguments

node

an object of class gdsn.class, a GDS node

compress

the compression method can be "" (no compression), "ZIP", "ZIP.fast", "ZIP.def", "ZIP.max" or "ZIP.none" (original zlib); "ZIP_RA", "ZIP_RA.fast", "ZIP_RA.def", "ZIP_RA.max" or "ZIP_RA.none" (zlib with efficient random access); "LZ4", "LZ4.none", "LZ4.fast", "LZ4.hc" or "LZ4.max" (LZ4 compression/decompression library); "LZ4_RA", "LZ4_RA.none", "LZ4_RA.fast", "LZ4_RA.hc" or "LZ4_RA.max" (with efficient random access). "LZMA", "LZMA.fast", "LZMA.def", "LZMA.max", "LZMA_RA", "LZMA_RA.fast", "LZMA_RA.def", "LZMA_RA.max" (lzma compression/decompression algorithm). See details

Details

Z compression algorithm (http://www.zlib.net) can be used to deflate the data stored in the GDS file. "ZIP" option is equivalent to "ZIP.def". "ZIP.fast", "ZIP.def" and "ZIP.max" correspond to different compression levels.

To support efficient random access of Z stream, "ZIP_RA", "ZIP_RA.fast", "ZIP_RA.def" or "ZIP_RA.max" should be specified. "ZIP_RA" option is equivalent to "ZIP_RA.def:256K". The block size can be specified by following colon, and "16K", "32K", "64K", "128K", "256K", "512K", "1M", "2M", "4M" and "8M" are allowed, like "ZIP_RA:64K". The compression algorithm tries to keep each independent compressed data block to be about of the specified block size, like 64K.

LZ4 fast lossless compression algorithm is allowed when compress="LZ4" (https://github.com/lz4/lz4). Three compression levels can be specified, "LZ4.fast" (LZ4 fast mode), "LZ4.hc" (LZ4 high compression mode), "LZ4.max" (maximize the compression ratio). The block size can be specified by following colon, and "64K", "256K", "1M" and "4M" are allowed according to LZ4 frame format. "LZ4" is equivalent to "LZ4.hc:256K".

To support efficient random access of LZ4 stream, "LZ4_RA", "LZ4_RA.fast", "LZ4_RA.hc" or "ZIP_RA.max" should be specified. "LZ4_RA" option is equivalent to "LZ4_RA.hc:256K". The block size can be specified by following colon, and "16K", "32K", "64K", "128K", "256K", "512K", "1M", "2M", "4M" and "8M" are allowed, like "LZ4_RA:64K". The compression algorithm tries to keep each independent compressed data block to be about of the specified block size, like 64K.

LZMA compression algorithm (https://tukaani.org/xz/) is available since gdsfmt_v1.7.18, which has a higher compression ratio than ZIP algorithm. "LZMA", "LZMA.fast", "LZMA.def" and "LZMA.max" available. To support efficient random access of LZMA stream, "LZMA_RA", "LZMA_RA.fast", "LZMA_RA.def" and "LZMA_RA.max" can be used. The block size can be specified by following colon. "LZMA_RA" is equivalent to "LZMA_RA.def:256K".

compression 1	compression 2	command line
ZIP	ZIP_RA	gzip -6
ZIP.fast	ZIP_RA.fast	gzip --fast
ZIP.def	ZIP_RA.def	gzip -6
ZIP.max	ZIP_RA.max	gzip --best
LZ4	LZ4_RA	LZ4 HC -6
LZ4.min	LZ4_RA.min	LZ4 fast 0
LZ4.fast	LZ4_RA.fast	LZ4 fast 2
LZ4.hc	LZ4_RA.hc	LZ4 HC -6
LZ4.max	LZ4_RA.max	LZ4 HC -9
LZMA	LZMA_RA	xz -6
LZMA.min	LZMA_RA.min	xz -0
LZMA.fast	LZMA_RA.fast	xz -2
LZMA.def	LZMA_RA.def	xz -6
LZMA.max	LZMA_RA.max	xz -9e
LZMA.ultra	LZMA_RA.ultra	xz --lzma2=dict=512Mi
LZMA.ultra_max	LZMA_RA.ultra_max	xz --lzma2=dict=1536Mi

Value

Return node.

Author(s)

Xiuwen Zheng

References

http://zlib.net, https://github.com/lz4/lz4, https://tukaani.org/xz/

See Also

readmode.gdsn, add.gdsn

Examples

# cteate a GDS file
f <- createfn.gds("test.gds")

n <- add.gdsn(f, "int.matrix", matrix(1:50*100, nrow=100, ncol=50))
n

compression.gdsn(n, "ZIP")

# close the GDS file
closefn.gds(f)

# delete the temporary file
unlink("test.gds", force=TRUE)

zhengxwen/gdsfmt documentation built on April 11, 2024, 3:19 a.m.