vcf_getChrom: Return a specific piece of information from the last line...
In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

	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 )

`vcffh`	VCF file handle
`fieldnam`	Name of a key of the key-value-pairs stored in the INFO subfield
`stridx`	Name of a sample

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.

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

Ulrich Wittelsbuerger

vcf_isSNP

	##
	##	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" )