seqRecompress {SeqArray}R Documentation

Recompress the GDS file

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

exclude

excluded GDS nodes

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.

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")

[Package SeqArray version 1.24.0 Index]