vcfwriter {vcfppR}

API for writing the VCF/BCF.

Description

Type the name of the class to see the details and methods

Value

A C++ class with the following fields/methods for writing the VCF/BCF

Fields

new

Constructor given a vcf file

• Parameter: vcffile - The path of a vcf file. don't start with "~"

• Parameter: version - The version of VCF specification

addContig

Add a Contig in the header of the vcf

• Parameter: str - A string for the CONTIG name

addFILTER

Add a FILTER in the header of the vcf

• Parameter: id - A string for the FILTER name

• Parameter: desc - A string for description of what it means

addINFO

Add a INFO in the header of the vcf

• Parameter: id - A string for the tag name

• Parameter: number - A string for the number

• Parameter: type - A string for the type

• Parameter: desc - A string for description of what it means

addFORMAT

Add a FORMAT in the header of the vcf

• Parameter: id - A string for the tag name

• Parameter: number - A string for the number

• Parameter: type - A string for the type

• Parameter: desc - A string for description of what it means

addSample

Add a SAMPLE in the header of the vcf

• Parameter: str - A string for a SAMPLE name

addLine

Add a line in the header of the vcf

• Parameter: str - A string for a line in the header of VCF

writeline

Write a variant record given a line

• Parameter: line - A string for a line in the variant of VCF. Not ended with "newline"

close

Close and save the vcf file

Examples

outvcf <- file.path(paste0(tempfile(), ".vcf.gz"))
bw <- vcfwriter$new(outvcf, "VCF4.1")
bw$addContig("chr20")
bw$addFORMAT("GT", "1", "String", "Genotype");
bw$addSample("NA12878")
s1 <- "chr20\t2006060\t.\tG\tC\t100\tPASS\t.\tGT\t1|0"
bw$writeline(s1)
bw$close()