Normalize a variant. Flip alleles if required and apply the normalization algorithm described at: https://genome.sph.umich.edu/wiki/Variant_Normalization Return Positive bitmask number in case of success, negative number in case of error. When positive, each bit has a different meaning when set, has defined by the NORM_* defines: * bit 0: Reference allele is inconsistent with the genome reference (i.e. when contains nucleotide letters other than A, C, G and T). * bit 1: Alleles have been swapped. * bit 2: Alleles nucleotides have been flipped (each nucleotide have been replaced with its complement). * bit 3: Alleles have been left extended. * bit 4: Alleles have been right trimmed. * bit 5: Alleles have been left trimmed.

Normalize a variant. Flip alleles if required and apply the normalization algorithm described at: https://genome.sph.umich.edu/wiki/Variant_Normalization Return Positive bitmask number in case of success, negative number in case of error. When positive, each bit has a different meaning when set, has defined by the NORM_* defines: * bit 0: Reference allele is inconsistent with the genome reference (i.e. when contains nucleotide letters other than A, C, G and T). * bit 1: Alleles have been swapped. * bit 2: Alleles nucleotides have been flipped (each nucleotide have been replaced with its complement). * bit 3: Alleles have been left extended. * bit 4: Alleles have been right trimmed. * bit 5: Alleles have been left trimmed.

NormalizeVariant(chrom, pos, ref, alt, mf = vk.env$genoref_$MF)

Arguments

chrom	Chromosome encoded number.
pos	Position. The reference position, with the first base having position 0.
ref	Reference allele. String containing a sequence of nucleotide letters.
alt	Alternate non-reference allele string.
mf	Memory-mapped file object as retured by MmapGenorefFile.