SeqArray (version 1.10.1)

seqStorage.Option: Storage and Compression Options for Importing VCF File(s)

Description

Storage and Compression Options for Importing VCF File(s).

Usage

seqStorage.Option(compression="ZIP_RA", float.mode="float32")

Arguments

compression

the default compression level, see add.gdsn for more options, e.g., "ZIP_RA", "ZIP_RA.max", "LZ4_RA", etc

float.mode

specify the storage mode for read numbers, e.g., "float32", "float64", "packedreal16"

Value

Return a list with a class name "SeqGDSStorageClass".

See Also

seqVCF2GDS

Examples

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

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

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

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


# close and remove
seqClose(f1)
seqClose(f2)
seqClose(f3)
unlink(c("tmp1.gds", "tmp2.gds", "tmp3.gds"))