seqMerge: Merge Multiple SeqArray GDS Files
In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

seqMerge

R Documentation

Merge Multiple SeqArray GDS Files

Description

Merges multiple SeqArray GDS files.

Usage

seqMerge(gds.fn, out.fn, storage.option="LZMA_RA", info.var=NULL, fmt.var=NULL,
    samp.var=NULL, optimize=TRUE, digest=TRUE, geno.pad=TRUE, verbose=TRUE)

Arguments

`gds.fn`	the file names of multiple GDS files
`out.fn`	the output file name
`storage.option`	specify the storage and compression option, "ZIP_RA" (`seqStorageOption("ZIP_RA")`); or "LZMA_RA" to use LZMA compression algorithm with higher compression ratio (by default)
`info.var`	characters, the variable name(s) in the INFO field; `NULL` for all variables, or `character()` excludes all INFO variables
`fmt.var`	characters, the variable name(s) in the FORMAT field; `NULL` for all variables, or `character()` excludes all FORMAT variables
`samp.var`	characters, the variable name(s) in 'sample.annotation'; or `NULL` for all variables
`optimize`	if `TRUE`, optimize the access efficiency by calling `cleanup.gds`
`digest`	a logical value (TRUE/FALSE) or a character ("md5", "sha1", "sha256", "sha384" or "sha512"); add md5 hash codes to the GDS file if TRUE or a digest algorithm is specified
`geno.pad`	TRUE, pad a 2-bit genotype array in bytes to avoid recompressing genotypes if possible
`verbose`	if `TRUE`, show information

Details

The function merges multiple SeqArray GDS files. Users can specify the compression method and level for the new GDS file. If gds.fn contains one file, users can change the storage type to create a new file.

WARNING: the functionality of seqMerge() is limited.

Value

Return the file name of GDS format with an absolute path.

Author(s)

Xiuwen Zheng

Examples

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

# the number of variants
total.count <- seqVCF_Header(vcf.fn, getnum=TRUE)$num.variant

split.cnt <- 5
start <- integer(split.cnt)
count <- integer(split.cnt)

s <- (total.count+1) / split.cnt
st <- 1L
for (i in 1:split.cnt)
{
    z <- round(s * i)
    start[i] <- st
    count[i] <- z - st
    st <- z
}

fn <- paste0("tmp", 1:split.cnt, ".gds")

# convert to 5 gds files
for (i in 1:split.cnt)
{
    seqVCF2GDS(vcf.fn, fn[i], storage.option="ZIP_RA",
        start=start[i], count=count[i])
}

# merge different variants
seqMerge(fn, "tmp.gds", storage.option="ZIP_RA")
seqSummary("tmp.gds")


####  merging different samples  ####

vcf.fn <- seqExampleFileName("gds")
file.copy(vcf.fn, "test.gds", overwrite=TRUE)

# modify 'sample.id'
seqAddValue("test.gds", "sample.id", paste0("S", 1:90), replace=TRUE)

# merging
seqMerge(c(vcf.fn, "test.gds"), "output.gds", storage.option="ZIP_RA")


# delete the temporary files
unlink(c("tmp.gds", "test.gds", "output.gds"), force=TRUE)
unlink(fn, force=TRUE)

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.