WhopGenome (version 0.9.4)

vcf_rule.setaction: Sets the kind of action to take when a rule matches (or does not match).

Description

The value that rule number should inspect is stored in the column named , e.g. "INFO" or "POS".

Usage

vcf_rule.setaction( vcffh, ruleidx, action )

Arguments

vcffh

VCF file handle

ruleidx

Filter rule to change

action

name of an action, see below

Value

TRUE on success, FALSE if it failed.

Details

Recognised values for 'action':

NOP do nothing SKIP drop line on match, read next line DROP KEEP keep line on match, do not test further SKIP_NOT drop line if not matching DROP_NOT SKIP_IF_NOT DROP_IF_NOT KEEP_NOT keep line if not matching rule, do not test further

Each action has also a 'disabled' variant, causing it to be ignored.

NOP_DISABLED SKIP_DISABLED DROP_DISABLED KEEP_DISABLED SKIP_NOT_DISABLED DROP_NOT_DISABLED KEEP_NOT_DISABLED

The _NOT / _IF_NOT variants effectively invert the comparison operation. (A == B) becomes (A != B), (1 <= 1="" a="" <="100)" becomes="" (a="" or=""> 100).

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.

Examples

	##
	##	Example:
	##
	vcffile <- vcf_open( system.file( "extdata" , "ex.vcf.gz" , package="WhopGenome" ) )
	vcf_addfilter( vcffile, "POS", "", "INT_CMP_OO",
					as.integer(49005), as.integer(49007), "DROP" )
	vcf_describefilters( vcffile )
	
	vcf_rule.setcolumn( vcffile , 0, "ID" )
	vcf_describefilters( vcffile )