seqStorageOption {SeqArray} | R Documentation |
Storage and compression options for GDS import and merging.
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, ...)
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" |
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.
Return a list with a class name "SeqGDSStorageClass", contains the compression algorithm for each data type.
Xiuwen Zheng
seqVCF2GDS
, seqRecompress
, seqMerge
# 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"))