vcf_rule.disable {WhopGenome} | R Documentation |
Filtering rules can be enabled and disabled. Disabled rules are ignored by any filtering VCF read function.
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 )