NAMESPACE

useDynLib(VariantAnnotation, .registration=TRUE)

import(methods)

import(BiocGenerics)

import(S4Vectors)

import(GenomeInfoDb)

import(GenomicRanges)

import(SummarizedExperiment)

import(Rsamtools)

import(zlibbioc)

importClassesFrom(Biobase, 
    AssayData
)

importFrom(Biobase,
    sampleNames, "sampleNames<-", samples
)

importClassesFrom(AnnotationDbi, 
    AnnotationDb
)

importMethodsFrom(AnnotationDbi, 
    colnames, exists, ncol, nrow,
    columns, keys, keytypes, select
)

importFrom(GenomicFeatures, 
    extractTranscriptSeqs, mapToTranscripts
)

importClassesFrom(GenomicFeatures, 
    TxDb
)

importMethodsFrom(GenomicFeatures, 
    cdsBy, exons, transcripts,
    fiveUTRsByTranscript, threeUTRsByTranscript,
    distance, mapToTranscripts
)

importFrom(IRanges, 
    CharacterList, IntegerList, 
    IRanges, LogicalList, NumericList, PartitioningByEnd, PartitioningByWidth,
    splitAsList, successiveViews, expand, endoapply
)

importClassesFrom(IRanges, 
    CharacterList, Ranges, RangesList, RangedData
)

importMethodsFrom(IRanges, 
    as.matrix, as.vector,
    countOverlaps, elementLengths, end, findOverlaps, 
    follow, gsub, lapply, narrow, order, 
    precede, rev, shift,
    split, start, "start<-",
    unlist, which, width, 
    expand
)

importFrom(XVector, "subseq", "subseq<-")

importFrom(Biostrings,
    AAStringSet, DNAStringSet, DNAStringSetList, DNA_BASES
)

importMethodsFrom(Biostrings,
    nchar, reverseComplement, substr, translate
)

importClassesFrom(Biostrings, 
    DNAStringSet, DNAStringSetList
)

importMethodsFrom(DBI, 
    dbCommit, dbConnect, dbDisconnect, dbExistsTable, 
    dbGetQuery, dbReadTable, dbWriteTable, dbListTables, 
    dbListFields
)

importClassesFrom(BSgenome, 
    BSgenome
)

importFrom(rtracklayer,
    liftOver
)

importFrom(utils, 
    txtProgressBar, setTxtProgressBar
)

exportClassPattern("^.*$")

export(
    VCF, VCFHeader, reference, 
    header, "header<-", meta, "meta<-",
    vcfWhich, "vcfWhich<-", vcfFixed, "vcfFixed<-", vcfInfo, "vcfInfo<-", 
    vcfGeno, "vcfGeno<-", vcfSamples, "vcfSamples<-", vcfTrimEmpty,
    "vcfTrimEmpty<-",
    duplicateRSID, CodingVariants, IntronVariants,
    FiveUTRVariants, ThreeUTRVariants, IntergenicVariants,
    SpliceSiteVariants, PromoterVariants, AllVariants,
    upstream, "upstream<-", downstream, "downstream<-",
    promoter, "promoter<-", intergenic, "intergenic<-",
    probabilityToSnpMatrix, GLtoGP, restrictToSNV,
    VRanges, VRangesList, asVCF, softFilter, resetFilter,
    totalDepth, altDepth, refDepth, sampleNames, "sampleNames<-", altFraction,
    softFilterMatrix, "softFilterMatrix<-", hardFilters, "hardFilters<-",
    called, stackSamples, "altDepth<-", "refDepth<-", "totalDepth<-",
    probabilityToSnpMatrix, GLtoGP,
    readInfo, readGeno, readGT, genotypeCodesToNucleotides,
    tabulate, VRangesScanVcfParam, readVcfAsVRanges,
    isSNV, isInsertion, isDeletion, isIndel, isDelins, isTransition,
    isSubstitution,
    VcfFile, VcfFileList,
    makeVRangesFromGRanges
)

exportMethods(
    filterVcf, scanVcf, scanVcfHeader, ScanVcfParam,
    readVcf, writeVcf, expand,
    readVcfLongForm, ## Defunct
    predictCoding, getTranscriptSeqs, 
    genotypeToSnpMatrix, snpSummary,
    locateVariants, summarizeVariants,
    isSNV, isInsertion, isDeletion, isIndel, isDelins, isTransition,
    isSubstitution,

    fixed, "fixed<-", ref, "ref<-", alt, "alt<-", qual, "qual<-",
    filt, "filt<-", info, "info<-", geno, "geno<-", strand, 
    "strand<-", "[", "[<-", cbind, rbind, "mcols<-", 

    genome, seqlevels, seqinfo,

    reference, samples, header, meta,

    keys, keytypes, columns, select
)