addOr                   Function to transform a large collapsed VCF
                        into a dataframe, incorporating predicted
                        states along with the log-likelihood ratio and
                        p-value.
addRatioDepth           Add depth ratios (inside vs outside events) per
                        sample
applyViterbi            Apply the hidden Markov model using the Viterbi
                        algorithm.
asDfVcf                 Function to transform a large collapsed VCF
                        into a dataframe with predicted states,
                        including chromosome, start position, end
                        position and metadata.
blocksVcf               Function to simplify contiguous variants with
                        the same state into blocks.
calculateEvents         Calculate UPD events in trio VCFs.
collapseEvents          Collapse events per sample and chromosome
hmm                     HMM data for predicting UPD events in trio
                        genomic data
identifyRecurrentRegions
                        Identify recurrent genomic regions across
                        samples
markRecurrentRegions    Annotate regions as recurrent or non-recurrent
processChromosome       Process a single chromosome for UPD detection
vcfCheck                Check quality parameters (optional) and change
                        IDs.
