Hapi-package            Hapi is a novel easy-to-use package that only
                        requires 3 to 5 gametes to reconstruct accurate
                        and high-resolution haplotypes of an
                        individual.  The gamete genotype data may be
                        generated from various platforms including
                        genotyping arrays and next generation
                        sequencing even with low-coverage.  Hapi simply
                        takes genotype data of known hetSNPs in single
                        gamete cells as input and report the
                        high-resolution haplotypes as well as
                        confidence level of each phased hetSNPs. The
                        package also includes a module allowing
                        downstream analyses and visualization of
                        crossovers in the gametes.
base2num                Convert genotype coded in A/T/C/G to 0/1
crossover               Crossover information across all gamete cells
gamete11                Haplotypes of a single gamete cell for
                        visualization
gmt                     Raw genotyping data
hapiAssemble            Consensus haplotype assembly
hapiAssembleEnd         Assembly of haplotypes in regions at the end of
                        a chromosome
hapiAutoPhase           Automatic inference of haplotypes
hapiBlockMPR            Maximum Parsimony of Recombination (MPR) for
                        proofreading of draft haplotypes
hapiCVCluster           Filter out hetSNPs in potential complex regions
hapiCVDistance          Histogram of crossover distance
hapiCVMap               Visualization of crossover map
hapiCVResolution        Histogram of crossover resolution
hapiFilterError         Filter out hetSNPs with potential genotyping
                        errors
hapiFrameSelection      Selection of hetSNPs to form a framework
hapiGameteView          Visualization of haplotypes in a single gamete
                        cell
hapiIdentifyCV          Indentify crossovers in gamete cells
hapiImupte              Imputation of missing genotypes in the
                        framework
hapiPhase               Phase draft haplotypes by majority voting
hg19                    Chromosome information of hg19
num2base                Convert genotype coded in 0/1 to A/T/C/G
