compression.gdsn: Modify compression mode
In gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) files
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Description
Modifie the compression mode of data field in the GDS node.
Usage
1
compression.gdsn(node, compress=c("", "ZIP", "ZIP_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.default", "ZIP.max" or "ZIP.none" (original
zlib); "ZIP_RA", "ZIP_RA.fast", "ZIP_RA.default", "ZIP_RA.max" or
"ZIP_RA.none" (zlib with efficient random access); "LZ4", "LZ4.none",
"LZ4.fast", "LZ4.hc" or "LZ4.max"; "LZ4_RA", "LZ4_RA.none",
"LZ4_RA.fast", "LZ4_RA.hc" or "LZ4_RA.max" (with efficient random
access). 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.default". "ZIP.fast", "ZIP.default" and "ZIP.max" correspond
to different compression levels.
To support efficient random access of Z stream, "ZIP_RA",
"ZIP_RA.fast", "ZIP_RA.default", "ZIP_RA.max" or "ZIP_RA.none" should
be specified. "ZIP_RA" option is equivalent to "ZIP_RA.default:256K".
The block size can be specified by following colon, and "16K", "32K",
"64K", "128K", "256K", "512K" and "1M" are allowed, such like
"ZIP_RA:16K". The compression algorithm tries to keep each
independent compressed data block to be about of the specified block
size, such like 64K.
LZ4 fast lossless compression algorithm is allowed with
compress="LZ4" (http://code.google.com/p/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", "ZIP_RA.max" or "LZ4_RA.none" 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" and "1M" are allowed, such like
"ZIP_RA:16K". The compression algorithm tries to keep each
independent compressed data block to be about of the specified block
size, such like 64K.
Value
Return node.
Author(s)
Xiuwen Zheng
References
http://github.com/zhengxwen/gdsfmt,
http://zlib.net/
See Also
gdsfmt documentation built on May 2, 2019, 4:41 p.m.
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Description Usage Arguments Details Value Author(s) References See Also
Description
Modifie the compression mode of data field in the GDS node.
Usage
1 | compression.gdsn(node, compress=c("", "ZIP", "ZIP_RA", "LZ4", "LZ4_RA"))
|
Arguments
node |
an object of class |
compress |
the compression method can be "" (no compression), "ZIP", "ZIP.fast", "ZIP.default", "ZIP.max" or "ZIP.none" (original zlib); "ZIP_RA", "ZIP_RA.fast", "ZIP_RA.default", "ZIP_RA.max" or "ZIP_RA.none" (zlib with efficient random access); "LZ4", "LZ4.none", "LZ4.fast", "LZ4.hc" or "LZ4.max"; "LZ4_RA", "LZ4_RA.none", "LZ4_RA.fast", "LZ4_RA.hc" or "LZ4_RA.max" (with efficient random access). 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.default". "ZIP.fast", "ZIP.default" and "ZIP.max" correspond to different compression levels.
To support efficient random access of Z stream, "ZIP_RA", "ZIP_RA.fast", "ZIP_RA.default", "ZIP_RA.max" or "ZIP_RA.none" should be specified. "ZIP_RA" option is equivalent to "ZIP_RA.default:256K". The block size can be specified by following colon, and "16K", "32K", "64K", "128K", "256K", "512K" and "1M" are allowed, such like "ZIP_RA:16K". The compression algorithm tries to keep each independent compressed data block to be about of the specified block size, such like 64K.
LZ4 fast lossless compression algorithm is allowed with
compress="LZ4" (http://code.google.com/p/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", "ZIP_RA.max" or "LZ4_RA.none" 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" and "1M" are allowed, such like "ZIP_RA:16K". The compression algorithm tries to keep each independent compressed data block to be about of the specified block size, such like 64K.
Value
Return node.
Author(s)
Xiuwen Zheng
References
http://github.com/zhengxwen/gdsfmt, http://zlib.net/
See Also
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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