# Imports (VariantAnnotation is a suggested package, loaded on demand for
#   VCF files and VCF objects)
import(methods)
import(gdsfmt)
import(SeqArray)
importFrom(utils, head, read.csv, untar, capture.output)
importFrom(IRanges, IRanges, which, start)
importFrom(S4Vectors, nrun, DataFrame, Rle, runLength, runValue)
importFrom(GenomicRanges, GRanges, GRangesList, seqnames)
importClassesFrom(IRanges, IRanges)
importClassesFrom(S4Vectors, DataFrame)
importClassesFrom(GenomicRanges, GRanges, GRangesList)

# Exports
export(
    seqAnnotate, seqAnnotateGDS, seqAnnotateVCF,
    seqAnnotList, seqValueCounts,
    seqFAVOR2GDS, seqFAVORTar2GDS, seqGnomAD2GDS,
    seqVEP2GDS, seqSnpEff2GDS, seqANNOVAR2GDS,
    seqAnnotStat, seqAnnotReport, seqAnnotGeneTable
)
exportMethods(seqAnnotate)

# S3 methods
S3method(print, SeqAnnotStat)
