R: Recompress the GDS file

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

Examples

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

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

unlink("tmp.gds")

[Package SeqArray version 1.26.2 Index]