NAMESPACE

import(RCurl)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(GenomicRanges)
import(Rsamtools)
import(GenomicAlignments)
import(Biostrings)
import(GenomicFeatures)
import(VariantAnnotation)
import(RSQLite)

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

importFrom("methods", "as", "is")
importFrom("utils", "download.file", "read.table", "write.table")

importFrom(AhoCorasickTrie, AhoCorasickSearchList)
importFrom(rtracklayer, browserSession, ucscTableQuery,
           tableNames, getTable, trackNames, ucscSchema)
importFrom(biomaRt, getBM, listAttributes, listDatasets, listMarts,
           useDataset, useMart)
		   
#importFrom(IRanges, DataFrame,  unlist,countOverlaps, 
#    findOverlaps, queryHits, values)		   

#importFrom(GenomicFeatures, cdsBy, exons, transcripts,
#    fiveUTRsByTranscript, threeUTRsByTranscript)

#importFrom(VariantAnnotation, scanVcf, scanVcfHeader, samples)		   

importFrom(AnnotationDbi, loadDb, saveDb)
importFrom(stringr, 'str_sub<-' )
importFrom(plyr, ddply, '.')

#importFrom(Biostrings,AAStringSet, DNAStringSet, reverseComplement,translate,
#	readBStringSet,readDNAStringSet)

	
export(PrepareAnnotationEnsembl,PrepareAnnotationRefseq,
    easyRun,easyRun_mul,
	calculateRPKM,Outputproseq,
	InputVcf, Varlocation, Positionincoding, aaVariation, 
    OutputVarproseq, OutputVarproseq_single, OutputVarprocodingseq, 
    Outputaberrant, 
    Bed2Range,JunctionType, OutputNovelJun,
 	OutputsharedPro, Multiple_VCF, SharedJunc
	)