R/variantkey.R
CheckReference.Rd
Check if the reference allele matches the reference genome data. Return Positive number in case of success, negative in case of error: * 0 the reference allele match the reference genome; * 1 the reference allele is inconsistent with the genome reference (i.e. when contains nucleotide letters other than A, C, G and T); * -1 the reference allele don't match the reference genome; * -2 the reference allele is longer than the genome reference sequence.
CheckReference(chrom, pos, ref, mf = vk.env$genoref_$MF)
chrom | Encoded Chromosome number (see encode_chrom). |
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pos | Position. The reference position, with the first base having position 0. |
ref | Reference allele. String containing a sequence of nucleotide letters. |
mf | Memory-mapped file object as retured by MmapGenorefFile. |