h5vc-package	h5vc-package
applyTallies	applyTallies
bases	mutationSpectrum
batchTallies	batchTallies
batchTallyParam	batchTallies
binGenome	binGenome
binnedAFs	binnedAFs
binnedCoverage	coverage
callDeletionsPaired	callVariants
callVariantsPaired	callVariants
callVariantsPairedFisher	callVariantsFisher
callVariantsSingle	callVariantsSingle
collectTallies	batchTallies
defineBlocks	helpers
encodeDNAString	helpers
formatGenomicPosition	helpers
geom_h5vc	geom_h5vc
getChromSize	helpers
getSampleData	getSampleData
h5dapply	h5dapply
h5dapply,GRanges-method	h5dapply
h5dapply,IRanges-method	h5dapply
h5dapply,numeric-method	h5dapply
h5readBlock	h5readBlock
h5vc	h5vc-package
mergeTallies	mergeTallies
mergeTallyFiles	mergeTallyFiles
mismatchPlot	mismatchPlot
mutationSpectrum	mutationSpectrum
plotMutationSpectrum	plotMutationSpectrum
prepareForHDF5	prepareForHDF5
prepareTallyFile	prepareTallyFile
rerunBatchTallies	batchTallies
resizeCohort	prepareTallyFile
setSampleData	getSampleData
tallyBAM	tallyBAM
tallyRanges	tallyRanges
tallyRangesBatch	tallyRanges
tallyRangesToFile	tallyRanges
variantCalls	mutationSpectrum
vcConfParams	callVariants
writeReference	writeReference
writeToTallyFile	writeToTallyFile
