vcf_getChrom: Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.

Description

Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.

Usage

vcf_getChrom( vcffh )
	vcf_getPos( vcffh )
	vcf_getID( vcffh )
	vcf_getRef( vcffh )
	vcf_getAlt( vcffh )
	vcf_getQual( vcffh )
	vcf_getFilter( vcffh )
	vcf_getInfo( vcffh )
	vcf_getInfoField( vcffh, fieldnam )
	vcf_getFormat( vcffh )
	vcf_getSample( vcffh, stridx )

Arguments

vcffh

VCF file handle

fieldnam

Name of a key of the key-value-pairs stored in the INFO subfield

stridx

Name of a sample

Value

None if the call failed, otherwise the respective data from the last read line is extracted.

Details

Use .Call("VCF_getChrom", filename ) to eliminate the overhead of using the R wrapper function. Replace getChrom by getPos, getID, getRef, getAlt, getQual, getFilter, getInfo, getInfoField, getSample and add the respective function arguments in the order given above to call the respective other function.

Examples

Run this code

	##
	##	Example:
	##
	vcffile <- vcf_open( system.file( "extdata", "ex.vcf.gz" , package="WhopGenome") )
	vcf_parseNextSNP( vcffile )
	vcf_getChrom( vcffile )
	vcf_getPos( vcffile )
	vcf_getID( vcffile )
	vcf_getAlt( vcffile )
	vcf_getQual( vcffile )
	vcf_getFilter( vcffile )
	vcf_getInfoField( vcffile, "AA" )