seqRecompress: Recompress the GDS file

In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description

Recompress the SeqArray GDS file.

Usage

seqRecompress(gds.fn, compress=c("ZIP", "LZ4", "LZMA", "Ultra", "UltraMax", "none"),
    exclude=character(), optimize=TRUE, verbose=TRUE)

Arguments

gds.fn	the file name of SeqArray file
compress	the compression method, compress="ZIP" by default
exclude	a list of GDS nodes to be excluded, see details
optimize	if TRUE, optimize the access efficiency by calling cleanup.gds
verbose	if TRUE, show information

Details

This function requires gdsfmt (>= v1.17.2). seqVCF2GDS usually takes lots of memory when the compression method "LZMA_RA.max", "Ultra" or "UltraMax" is specified. So users could call seqVCF2GDS(, storage.option="ZIP_RA") first, and then recompress the GDS file with a higher compression option, e.g., "UltraMax". seqRecompress() takes much less memory, since it recompresses data in a GDS node each time.

ls.gdsn(gdsfile, include.hidden=TRUE, recursive=TRUE) returns a list of GDS nodes to be re-compressed, and users can specify the excluded nodes in the argument exclude.

Value

None.

Author(s)

Xiuwen Zheng

See Also

seqVCF2GDS, seqStorageOption

Examples

gds.fn <- seqExampleFileName("gds")
file.copy(gds.fn, "tmp.gds")

seqRecompress("tmp.gds", "LZMA")

unlink("tmp.gds")

SeqArray documentation built on Nov. 8, 2020, 5:08 p.m.