applyTallies            Preparing the results of tallyBAM for writing
                        to an HDF5 tally file
batchTallies            Tallying bam files in parallel using
                        'BatchJobs' on high performance compute
                        clusters (HPC)
binGenome               Function for binning a genome.
binnedAFs               Estimate allelic frequency distributions in
                        bins along the genome
binnedCoverage          Coverage analysis
callVariantsPaired      Variant calling
callVariantsPairedFisher
                        Paired variant calling using fisher tests
callVariantsSingle      Single sample variant calling
formatGenomicPosition   helper functions
geom_h5vc               geom_h5vc
getSampleData           Reading and writing sample data from / to a
                        tally file
h5dapply                h5dapply
h5readBlock             h5readBlock
h5vc-package            Managing alignment tallies using a hdf5 backend
mergeTallies            Merging the prepared results from multiple bam
                        file tallies into one block that can be written
                        to the HDF5 tally file
mergeTallyFiles         Merging multiple tally files into one
mismatchPlot            mismatchPlot
mutationSpectrum        Mutation spectrum analyses
plotMutationSpectrum    Plotting a mutation spectrum
prepareForHDF5          Preparing the results of tallyBAM for writing
                        to an HDF5 tally file
prepareTallyFile        prepareTallyFile
tallyBAM                tallyBAM
tallyRanges             Tallying function with a 'GRanges' interface.
writeReference          Filling the Reference dataset in a tally file
                        from a DNAString
writeToTallyFile        Writing data to an HDF5 tally file
