shard.vcf: Splits a vcf file into many smaller files for easy...

In erickramer/batch.vcf: What the package does (short line)

Usage

shard.vcf(vcf.file, n = 1e+05, directory = NULL)

Arguments

vcf.file
n
directory

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (vcf.file, n = 1e+05, directory = NULL) 
{
    write.file = function(f, file.list = c()) {
        tmpdir = paste(directory, "/", "part", floor(length(file.list)/100), 
            sep = "")
        if (!file.exists(tmpdir)) 
            dir.create(tmpdir)
        lines = scanTabix(f)[[1]]
        if (length(lines) > 0) {
            output.file = paste(tempfile(tmpdir = tmpdir), ".vcf.gz", 
                sep = "")
            o = pipe(paste("bgzip -c >", output.file, sep = ""), 
                open = "w")
            writeLines(header, o)
            writeLines(lines, o)
            close(o)
            write.file(f, file.list = c(file.list, output.file))
        }
        else file.list
    }
    index.file = function(filename) {
        system(paste("tabix", filename))
        filename
    }
    if (!file.exists(paste(vcf.file, "tbi", sep = ""))) 
        index.file(vcf.file)
    directory = if (is.null(directory)) 
        gsub(".vcf.gz$", "", vcf.file)
    else directory
    if (!file.exists(directory)) 
        dir.create(directory)
    header = headerTabix(vcf.file)$header
    f = TabixFile(vcf.file, yieldSize = n)
    open(f)
    files = write.file(f)
    close(f)
    sapply(files, index.file)
  }

erickramer/batch.vcf documentation built on May 16, 2019, 8:28 a.m.