WhopGenome (version 0.9.4)

vcf_rule.setrefvalues: Set reference values for a filtering rule's comparison operation.

Description

Set the reference values 1 and 2 for the comparison operation of rule . Soem comparison operations need only the first reference value and ignore .

Usage

vcf_rule.setrefvalues( vcffh, ruleidx, ref1, ref2 )

Arguments

vcffh

VCF file handle

ruleidx

name of column containing the to-be-checked values

ref1

name of the subfield or "" to check

ref2

Type of comparison to perform. See Details

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_setregion(vcffile, "Y", 50000, 51000 )
	
	#
	# USELESS filter : # filter out SNPs with rule  "DROP if (0.0 < INFO:AF < 0.2)"
	#	pos 50001 has AF=0.285 , for which (0 < 0.285 < 0.2) is true 
	#
	vcf_addfilter( vcffile, "INFO", "AF", "FLT_CMP_OO", 0, 0.2, "DROP" )
	vcf_describefilters( vcffile )
	
	vcf_readLineVecFiltered( vcffile )	# pos 50001
	vcf_readLineVecFiltered( vcffile )	# pos 50002
	
	#
	#
	vcf_setregion(vcffile, "Y", 50000, 51000 )
	
	#CORRECT rule:
	# filter out SNP at pos 50001 with INFO:AF=0.285 with rule  "DROP if (0.2 < INFO:AF < 0.3)"
	#
	vcf_rule.setrefvalues( vcffile , 0 , 0.2, 0.3 )
	vcf_describefilters( vcffile )
	
	vcf_readLineVecFiltered( vcffile )	# pos 50002
	vcf_readLineVecFiltered( vcffile )	# pos 50003