vcf_rule.setcomparison: Set comparison operation for filtering rule.
In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description Usage Arguments Details Value Author(s) Examples

For filtering rule <ruleidx> the comparison operation is set to <cmpop>, which is one of the following strings:
string: alternative: meaning:
——- ———— ——– "HASKEY" "DOES_EXIST" key (specified as field) is present in column
- integer comparisons:
"INT=" "INT_CMP" ref1 = value
"INT()" "INT_CMP_OO" ref1 < value < ref2
"INT(]" "INT_CMP_OC" ref1 < value <= ref2
"INT[)" "INT_CMP_CO" ref1 <= value < ref2
"INT[]" "INT_CMP_CC" ref1 <= value <= ref2

- floating point (real numbers):
"FLT==" "FLT_CMP" ref1 = value FLT_CMP
"FLT()" "FLT_CMP_OO" ref1 < value < ref2
"FLT(]" "FLT_CMP_OC" ref1 < value <= ref2
"FLT[)" "FLT_CMP_CO" ref1 <= value < ref2
"FLT[]" "FLT_CMP_CC" ref1 <= value <= ref2

1	vcf_rule.setcomparison( vcffh, ruleidx, cmpop )

`vcffh`	VCF file handle
`ruleidx`	number of rule in list
`cmpop`	One of the above strings, naming the comparison operation to perform

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 on success, FALSE if it failed.

Ulrich Wittelsbuerger

	##
	##	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.setcomparison( vcffile , 0, "INT_CMP_CC" )
	vcf_describefilters( vcffile )