NAMESPACE

useDynLib(GoogleGenomics, .registration = TRUE, .fixes = "C_")

## API related imports ##
import(httr)
import(methods)
importFrom(rjson, fromJSON, toJSON)

## Bioc utility functions and S4 constructors ##
import(S4Vectors)
importFrom(Biobase, "sampleNames<-")
importFrom(Biostrings, DNAStringSet, DNAStringSetList)
importFrom(GenomeInfoDb, "seqlevelsStyle<-")
importFrom(GenomicAlignments, GAlignments)
importFrom(GenomicRanges, GRanges)
importFrom(IRanges, IRanges)
importFrom(Rsamtools, bamFlagAsBitMatrix)
importFrom(VariantAnnotation, strand, VRanges)

## Utility imports ##
importFrom(utils, installed.packages)

#### Exports ####

## Authentication ##
export(authenticate)
export(defaultGcloudCredsPath)

## Generic Search ##
export(getSearchPage)

## gRPC ##
export(callGRPCMethod)
export(getRProtoBufDefaultObject)
export(isGRPCAvailable)

## Reads ##
export(getReadsPage)
export(getReads)
export(readsToGAlignments)

## Variants ##
export(getVariantsPage)
export(getVariantCalls)
export(getVariants)
export(variantsToGRanges)
export(variantsToVRanges)