Reference

All functions
AreOverlappingRegionKeys()	Check if two regionkeys are overlapping. Return 1 if the regions overlap, 0 otherwise.
AreOverlappingRegionRegionKey()	Check if a region and a regionkey are overlapping. Return 1 if the regions overlap, 0 otherwise.
AreOverlappingRegions()	Check if two regions are overlapping. Return 1 if the regions overlap, 0 otherwise.
AreOverlappingVariantKeyRegionKey()	Check if variantkey and regionkey are overlapping. Return 1 if the regions overlap, 0 otherwise.
CheckReference()	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.
CloseVariantKey()	Unmap the memory-mapped files. This should be the last function called in order to close any open memory-mapped file.
CompareVariantKeyChrom()	Compares two VariantKeys by chromosome only. Returns -1 if the first chromosome is smaller than the second, 0 if they are equal and 1 if the first is greater than the second.
CompareVariantKeyChromPos()	Compares two VariantKeys by chromosome and position. Return -1 if the first CHROM+POS is smaller than the second, 0 if they are equal and 1 if the first is greater than the second.
DecodeChrom()	Decode the CHROM code.
DecodeRefAlt()	Decode the 32 bit REF+ALT code if reversible (if it has 11 or less bases in total and only contains ACGT letters).
DecodeRegionKey()	Decode a RegionKey code and returns the components as regionkey_t structure.
DecodeRegionStrand()	Decode the strand direction code (0 > 0, 1 > +1, 2 > -1).
DecodeStringID()	Decode the encoded string ID. This function is the reverse of encode_string_id. The string is always returned in uppercase mode.
DecodeVariantKey()	Decode a VariantKey code and returns the components.
EncodeChrom()	Returns chromosome encoding.
EncodeRefAlt()	Returns reference+alternate encoding.
EncodeRegionKey()	Returns a 64 bit regionkey
EncodeRegionStrand()	Encode the strand direction (-1 > 2, 0 > 0, +1 > 1).
EncodeStringID()	Encode maximum 10 characters of a string into a 64 bit unsigned integer. This function can be used to convert generic string IDs to numeric IDs.
EncodeStringNumID()	Encode a string composed by a character section followed by a separator character and a numerical section into a 64 bit unsigned integer. For example: "ABCDE:0001234" Encodes up to 5 characters in uppercase, a number up to 2^27, and up to 7 zero padding digits. If the string is 10 character or less, then the EncodeStringID() is used.
EncodeVariantKey()	Returns a 64 bit variant key based on pre-encoded CHROM, POS (0-base) and REF+ALT.
ExtendRegionKey()	Extend a regionkey region by a fixed amount from the start and end position.
ExtractRegionKeyChrom()	Extract the CHROM code from RegionKey.
ExtractRegionKeyEndPos()	Extract the END POS code from RegionKey.
ExtractRegionKeyStartPos()	Extract the START POS code from RegionKey.
ExtractRegionKeyStrand()	Extract the STRAND from RegionKey.
ExtractVariantKeyChrom()	Extract the CHROM code from VariantKey.
ExtractVariantKeyPos()	Extract the POS code from VariantKey.
ExtractVariantKeyRefAlt()	Extract the REF+ALT code from VariantKey.
FindAllRvVariantKeyByRsid()	Search for the specified rsID and returns all the associated VariantKeys in the RV file. NOTE: the output is limited to maximum 10 results.
FindAllVrRsidByVariantKey()	Search for the specified VariantKey and returns all the associated rsIDs in the VR file. NOTE: the output is limited to maximum 10 results.
FindRefAltByVariantKey()	Retrieve the REF and ALT strings for the specified VariantKey. Return REF+ALT length or 0 if the VariantKey is not found.
FindRvVariantKeyByRsid()	Search for the specified rsID and returns the first occurrence of VariantKey in the RV file, or zero if not found.
FindVrChromposRange()	Search for the specified CHROM-POS range and returns the first occurrence of rsID in the VR file.
FindVrRsidByVariantKey()	Search for the specified VariantKey and returns the first occurrence of rsID in the VR file, or 0 if not found.
FlipAllele()	Flip the allele nucleotides (replaces each letter with its complement). The resulting string is always in uppercase. Support extended nucleotide letters.
GetGenorefSeq()	Returns the genome reference nucleotide at the specified chromosome and position.
GetNextRvVariantKeyByRsid()	Get the next VariantKey for the specified rsID in the RV file, or 0 if not found This function can be called in a loop to get all VariantKeys that are associated with the same rsID (if any).
GetNextVrRsidByVariantKey()	Get the next rsID for the specified VariantKey in the VR file, or 0 if not found This function can be called in a loop to get all rsIDs that are associated with the same VariantKey (if any).
GetRegionKeyChromEndPos()	Get the CHROM + END POS encoding from RegionKey.
GetRegionKeyChromStartPos()	Get the CHROM + START POS encoding from RegionKey.
GetVariantKeyChromEndPos()	Get the CHROM + END POS encoding from VariantKey.
GetVariantKeyChromStartPos()	Get the CHROM + START POS encoding from VariantKey.
GetVariantKeyEndPos()	Get the VariantKey end position (POS + REF length). Return variant end position.
GetVariantKeyRefLength()	Retrieve the REF length for the specified VariantKey. Return REF length or 0 if the VariantKey is not reversible and not found.
HashStringID()	Hash the input string into a 64 bit unsigned integer. This function can be used to convert long string IDs to numeric IDs.
InitVariantKey()	Load the VariantKey support files. This should be the first function called in order to load the support files.
MmapGenorefFile()	Memory map the specified genome reference binary file (fasta.bin). Returns the memory mapped file object, the columns object and the number of rows.
MmapNRVKFile()	Memory map the specified NRVK binary file (nrvk.bin). Returns the memory mapped file object, the columns object and the number of rows.
MmapRSVKFile()	Memory map the specified RSVK binary file (rsvk.bin). Returns the memory mapped file object, the columns object and the number of rows.
MmapVKRSFile()	Memory map the specified VKRS binary file (vkrs.bin). Returns the memory mapped file object, the columns object and the number of rows.
MunmapBinfile()	Unmap and close the memory-mapped file. On success, munmap() returns 0, on failure -1.
NormalizeVariant()	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.
NormalizedVariantKey()	Create a normalized variantkey.
ParseRegionKeyHex()	Parses a RegionKey hexadecimal string and returns the code.
ParseVariantKeyHex()	Parses a VariantKey hexadecimal string and returns the code.
RegionKey()	Returns a 64 bit regionkey based on CHROM, START POS (0-based), END POS and STRAND.
RegionKeyHex()	Returns RegionKey hexadecimal string (16 characters).
ReverseRegionKey()	Reverse a RegionKey code and returns the normalized components as regionkey_rev_t structure.
ReverseVariantKey()	Reverse a VariantKey code and returns the normalized components.
VariantKey()	Returns a 64 bit variant key based on CHROM, POS (0-base), REF, ALT. The variant should be already normalized (see NormalizeVariant or use NormalizedVariantkey).
VariantKeyHex()	Returns VariantKey hexadecimal string (16 characters).
VariantKeyRange()	Returns minimum and maximum variant keys for range searches.
VariantToRegionkey()	Get RegionKey from VariantKey.
VknrBinToTsv()	Convert a vrnr.bin file to a simple TSV. Return Number of written bytes or 0 in case of error. For the reverse operation see the resources/tools/nrvk.sh script.
as.character(<hex64>)	Coerce hex64 vector to decimal character
as.character(<uint64>)	Coerce uint64 vector to character
as.data.frame(<uint64>)	Coerce uint64 vector to data.frame.
as.hex64(<>)	Coerce from NULL to hex64.
as.hex64()	Coerce to hex64.
as.hex64(<character>)	Coerce character vector to hex64
as.hex64(<factor>)	Coerce from factor to hex64.
as.hex64(<hex64>)	Coerce from hex64 to hex64.
as.hex64(<uint64>)	Convert uint64 vector to hex64.
as.uint64(<>)	Coerce from NULL to uint64.
as.uint64()	Coerce to uint64.
as.uint64(<character>)	Coerce character vector to uint64
as.uint64(<double>)	Coerce double vector to uint64
as.uint64(<factor>)	Coerce from factor to uint64.
as.uint64(<hex64>)	Convert hexadecimal character vector to uint64.
as.uint64(<integer>)	Coerce integer vector to uint64
as.uint64(<uint64>)	Coerce from uint64 to uint64.
c(<uint64>)	Concatenate uint64 vectors.
cbind(<uint64>)	Combine uint64 vectors by columns.
`==`(<uint64>)	Returns true if x and y are equal.
format(<uint64>)	Format uint64 vector for pretty printing.
`>`(<uint64>)	Returns true if x is greater than y.
`>=`(<uint64>)	Returns true if x is greater or equal than y.
hex64()	Create a new hex64 vector.
identical.hex64()	Identity function for class hex64.
identical.uint64()	Identity function for class uint64.
intersect.uint64()	Returns the intersection of two sorted uint64 vectors.
is.hex64()	Check if the object x is of hex64 class.
is.uint64()	Check if the object x is of uint64 class.
`length<-`(<uint64>)	Set the length of uint64 vector.
`<`(<uint64>)	Returns true if x is less than y.
`<=`(<uint64>)	Returns true if x is less or equal than y.
`!=`(<uint64>)	Returns true if x and y are different.
order.uint64()	Returns a permutation which rearranges its first argument into ascending order.
print(<uint64>)	Prints uint64 argument and returns it invisibly.
rbind(<uint64>)	Combine uint64 vectors by rows.
rep(<uint64>)	Replicate elements of uint64 vectors.
rev(<uint64>)	Reverse a uint64 vector.
sort(<uint64>)	Sorts a uint64 vector in ascending order.
`[`(<uint64>)	Extract uint64 vector parts
`[[`(<uint64>)	Extract uint64 vector parts
`[[<-`(<uint64>)	Replace parts of uint64 vector
`[<-`(<uint64>)	Replace parts of uint64 vector
uint64()	Create a new uint64 vector.
union.uint64()	Returns the union of two sorted uint64 vectors.
unique(<uint64>)	Eliminates all but the first element from every consecutive group of equal values.