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.

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)

Arguments

chrom	Encoded Chromosome number (see encode_chrom).
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.