Managing alignment tallies using a hdf5 backend

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Documentation for package ‘h5vc’ version 2.38.0

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

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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