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, `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")

[Package SeqArray version 1.30.0 Index]