vcf_rule.disable: Disable and enable processing of a rule
In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description Usage Arguments Details Value Author(s) Examples

Filtering rules can be enabled and disabled. Disabled rules are ignored by any filtering VCF read function.

1 2	vcf_rule.disable( vcffh, ruleidx ) vcf_rule.enable( vcffh, ruleidx )

`vcffh`	VCF file handle
`ruleidx`	number of rule

Certain VCF read functions support the fast pre-filtering mechanism of WhopGenome. The pre-filtering mechanism is a list of rules that describe how and what to check in SNP descriptions and is executed very quickly without using any R code. Every rule specifies the column of data (e.g. INFO, POS, FILTER), the key in the column (e.g. AF in the INFO column), the type of comparison , reference values to compare against and whether to keep or drop the line if the rule matches.

TRUE if succeeded, FALSE if not

Ulrich Wittelsbuerger

	##
	##	Example:
	##
	vcffile <- vcf_open( system.file( "extdata" , "ex.vcf.gz" , package="WhopGenome" ) )
	vcf_setregion(vcffile, "Y", 1, 100000 )
	vcf_addfilter( vcffile, "POS", "", "INT_CMP_OO",
					as.integer(49005), as.integer(49007), "DROP" )
	vcf_describefilters( vcffile )
	vcf_readLineVecFiltered( vcffile )

	vcf_rule.disable( vcffile, 0 )
	vcf_describefilters( vcffile )
	vcf_restartregion( vcffile )
	vcf_readLineVecFiltered( vcffile )