seqStorageOption {SeqArray} | R Documentation

## Storage and Compression Options

### Description

Storage and compression options for GDS import and merging.

### Usage

    seqStorageOption(compression=c("ZIP_RA", "ZIP_RA.fast", "ZIP_RA.max", "LZ4_RA",
        "LZ4_RA.fast", "LZ4_RA.max", "LZMA_RA", "LZMA_RA.fast", "LZMA_RA.max",
        "Ultra", "UltraMax", "none"), mode=NULL, float.mode="float32",
        geno.compress=NULL, info.compress=NULL, format.compress=NULL,
        index.compress=NULL, ...)

### Arguments

`compression` | the default compression level ("ZIP_RA"), see add.gdsn for the description of compression methods
`mode` | a character vector, specifying storage type for corresponding variable, e.g., c('annotation/info/HM'="int16", 'annotation/format/PL'="int")
`float.mode` | specify the storage mode for read numbers, e.g., "float32", "float64", "packedreal16"; the additional parameters can follow by colon, like "packedreal16:scale=0.0001"
`geno.compress` | NULL for the default value, or the compression method for genotypic data
`info.compress` | NULL for the default value, or the compression method for data sets stored in the INFO field (i.e., "annotation/info")
`format.compress` | NULL for the default value, or the compression method for data sets stored in the FORMAT field (i.e., "annotation/format")
`index.compress` | NULL for the default value, or the compression method for data index variables (e.g., "annotation/info/@HM")
`...` | other specified storage compression for corresponding variable, e.g., 'annotation/info/HM'="ZIP_MAX"

### Details

The compression modes `"Ultra"` and `"UltraMax"` attempt to maximize the compression ratio using gigabyte-sized or even terabyte-sized virtual memory, according to `"LZMA_RA.ultra"` and `"LZMA_RA.ultra_max"` in `compression.gdsn`. These features require gdsfmt (>=v1.16.0). `"Ultra"` and `"UltraMax"` may not increase the compression ratio much compared with `"LZMA_RA.max"`, and these options are designed for the users who want to exhaust the computational resources.

### Value

Return a list with a class name "SeqGDSStorageClass", contains the compression algorithm for each data type.

### Author(s)

Xiuwen Zheng

### See Also

`seqVCF2GDS`, `seqRecompress`, `seqMerge`

### Examples

    # the file of VCF
    (vcf.fn <- seqExampleFileName("vcf"))

    # convert
    seqVCF2GDS(vcf.fn, "tmp1.gds", storage.option=seqStorageOption())
    (f1 <- seqOpen("tmp1.gds"))

    # convert (maximize the compression ratio)
    seqVCF2GDS(vcf.fn, "tmp2.gds", storage.option=seqStorageOption("ZIP_RA.max"))
    (f2 <- seqOpen("tmp2.gds"))

    # does not compress the genotypic data
    seqVCF2GDS(vcf.fn, "tmp3.gds", storage.option=
        seqStorageOption("ZIP_RA", geno.compress=""))
    (f3 <- seqOpen("tmp3.gds"))

    # compress with LZ4
    seqVCF2GDS(vcf.fn, "tmp4.gds", storage.option=seqStorageOption("LZ4_RA"))
    (f4 <- seqOpen("tmp4.gds"))

    # close and remove the files
    seqClose(f1)
    seqClose(f2)
    seqClose(f3)
    seqClose(f4)

    unlink(c("tmp1.gds", "tmp2.gds", "tmp3.gds", "tmp4.gds"))

[Package SeqArray version 1.28.1 Index]