seqMerge: Merge Multiple SeqArray GDS Files

Description

Merges multiple SeqArray GDS files.

Usage

seqMerge(gds.fn, out.fn, storage.option="ZIP_RA", info.var=NULL, fmt.var=NULL, samp.var=NULL, optimize=TRUE, digest=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 options, by default seqStorageOption("ZIP_RA"); or "LZMA_RA" to use LZMZ compression algorithm with higher compression ratio

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 hash codes to the GDS file if TRUE or a digest algorithm is specified

verbose

if TRUE, show information

Value

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

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.

Examples

Run this code

# 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], start=start[i], count=count[i])

# merge
seqMerge(fn, "tmp.gds")
seqSummary("tmp.gds")


####

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

# modify 'sample.id'
f <- openfn.gds("test.gds", FALSE)
sid <- read.gdsn(index.gdsn(f, "sample.id"))
add.gdsn(f, "sample.id", paste("S", 1:length(sid)), replace=TRUE)
closefn.gds(f)

# merging
seqMerge(c(vcf.fn, "test.gds"), "output.gds")



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