WhopGenome (version 0.9.4)

vcf_rule.setcolumn: Set column a rule should examine.

Description

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

Usage

vcf_rule.setcolumn( vcffh, ruleidx, column )

Arguments

vcffh

VCF file handle

ruleidx

Filter rule to change

column

name of column containing the to-be-checked values

Value

TRUE on success, FALSE if it failed.

Details

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 )