AlleleCodeBuf           Returns an empty two-row numeric matrix that
                        ReadAlleles() can load to.
BoolBuf                 Returns a bool buffer that ReadAlleles() can
                        load phasing information to.
Buf                     Returns a numeric buffer that Read() or
                        ReadHardcalls() can load to.
ClosePgen               Closes a pgen object, releasing resources.
ClosePvar               Closes a pvar object, releasing memory.
GetAlleleCode           Look up an allele code.
GetAlleleCt             Returns the effective number of alleles for a
                        variant.  Note that if no pvar was provided to
                        the NewPgen() call, this function may return 2
                        even at multiallelic variants, since the .pgen
                        may not store allele-count information.
GetMaxAlleleCt          Returns the maximum GetAlleleCt() value across
                        all variants in the file.
GetRawSampleCt          Returns the number of samples in the file.
GetVariantChrom         Retrieve chromosome ID for given variant index.
GetVariantCt            Returns the number of variants in the file.
GetVariantId            Convert variant index to variant ID string.
GetVariantPos           Retrieve POS (base-pair coordinate on a
                        chromosome) for given variant index.
GetVariantsById         Convert variant ID string to variant index(es).
HardcallPhasePresent    Returns whether explicitly phased hardcalls are
                        present.
HasSparse               Returns whether dosages for the variant_numth
                        variant and given allele are represented in a
                        sparse manner that is supported by
                        ReadSparse(), under the current sample subset.
HasSparseHardcalls      Returns whether hardcalls for the variant_numth
                        variant and given allele are represented in a
                        sparse manner that is supported by
                        ReadSparseHardcalls().
IntAlleleCodeBuf        Returns an empty two-row integer matrix that
                        ReadAlleles() can load to.
IntBuf                  Returns an integer buffer that ReadHardcalls()
                        can load to.
NewPgen                 Opens a .pgen or PLINK 1 .bed file.
NewPvar                 Loads variant positions, IDs, and allele codes
                        from a .pvar or .bim file (which can be
                        compressed with gzip or Zstd).
Read                    Loads the variant_numth variant, and then fills
                        buf with numeric dosages in [0, 2] indicating
                        the dosages of the first ALT (or
                        user-specified) allele for each sample, with
                        missing values represented by NA.
ReadAlleles             Loads the variant_numth variant, and then fills
                        acbuf with integer allele codes, where each
                        column of the buffer corresponds to a sample.
                        An allele code of 0 corresponds to the REF
                        allele, 1 to the first ALT, 2 to the second
                        ALT, etc.  Missing hardcalls are represented by
                        a pair of NA codes.
ReadHardcalls           Loads the variant_numth variant, and then fills
                        buf with {0, 1, 2, NA} values indicating the
                        number of copies of the first ALT (or
                        user-specified) allele each sample has.
ReadIntList             Load hardcalls for multiple variants as an
                        integer matrix.
ReadList                Load dosages for multiple variants as a numeric
                        matrix.
ReadSparse              If HasSparse() is true, returns a sparse
                        representation for the (variant, allele) pair.
                        If HasSparse() is false, the function fails.
ReadSparseHardcalls     If HasSparseHardcalls() is true, returns a
                        sparse representation for the (variant, allele)
                        pair.  If HasSparseHardcalls() is false, the
                        function fails.
VariantScores           Compute variant scores.
pgenlibr-package        PLINK 2 Binary (.pgen) Reader
