# Managing alignment tallies using a hdf5 backend

## Documentation for package ‘h5vc’ version 2.8.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

h5vc-package | Managing alignment tallies using a hdf5 backend
applyTallies | Preparing the results of tallyBAM for writing to an HDF5 tally file
bases | Mutation spectrum analyses
batchTallies | Tallying bam files in parallel using 'BatchJobs' on high performance compute clusters (HPC)
batchTallyParam | 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
callDeletionsPaired | Variant calling
callVariantsPaired | Variant calling
callVariantsPairedFisher | Paired variant calling using fisher tests
callVariantsSingle | Single sample variant calling
collectTallies | Tallying bam files in parallel using 'BatchJobs' on high performance compute clusters (HPC)
defineBlocks | helper functions
encodeDNAString | helper functions
formatGenomicPosition | helper functions
geom_h5vc | geom_h5vc
getChromSize | helper functions
getSampleData | Reading and writing sample data from / to a tally file
h5dapply | h5dapply
h5dapply-method | h5dapply
h5readBlock | h5readBlock
h5vc | 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
rerunBatchTallies | Tallying bam files in parallel using 'BatchJobs' on high performance compute clusters (HPC)
resizeCohort | prepareTallyFile
setSampleData | Reading and writing sample data from / to a tally file
tallyBAM | tallyBAM
tallyRanges | Tallying function with a 'GRanges' interface.
tallyRangesBatch | Tallying function with a 'GRanges' interface.
tallyRangesToFile | Tallying function with a 'GRanges' interface.
variantCalls | Mutation spectrum analyses
vcConfParams | Variant calling
writeReference | Filling the Reference dataset in a tally file from a DNAString
writeToTallyFile | Writing data to an HDF5 tally file