import(methods)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomicRanges)


importMethodsFrom(GenomicFeatures, genes)


importFrom(rtracklayer, ucscGenomes)
importFrom(stringr, str_count)

importFrom(mclust, Mclust)
importFrom(mclust, mclustBIC)

importFrom(foreach, foreach)
importFrom(foreach, "%dopar%")

importFrom(rtracklayer, export)

importFrom(GenomicFeatures, supportedUCSCtables)
importFrom(GenomicFeatures, makeTxDbFromUCSC)
importFrom(GenomicFeatures, cdsBy)
importFrom(GenomicFeatures, genes)
importFrom(GenomicFeatures, intronsByTranscript)
importFrom(GenomicFeatures, threeUTRsByTranscript)
importFrom(GenomicFeatures, fiveUTRsByTranscript)

importFrom(ggplot2, ggplot)
importFrom(ggplot2, aes)
importFrom(ggplot2, geom_point)
importFrom(ggplot2, facet_grid)
importFrom(ggplot2, theme_bw)
importFrom(ggplot2, labs)
importFrom(ggplot2, theme)
importFrom(ggplot2, element_text)
importFrom(ggplot2, rel)
importFrom(ggplot2, xlab)
importFrom(ggplot2, ylab)
importFrom(ggplot2, geom_smooth)

importFrom(Hmisc, dotchart2)

importFrom(seqinr, write.fasta)

importFrom(Biostrings, getSeq)
importFrom(Biostrings, complement)

importFrom(Rsamtools, ScanBamParam)
importFrom(Rsamtools, scanBam)

export( 
	readSortedBam,
	getAllSub,
	fitMixtureModel,
	getExpInterval,
	getHighConfSub,
	getClusters,
	filterClusters,
	annotateClusters,
	plotSizeDistribution,
	plotStatistics,
	getMetaGene,
	getMetaTSS,
	plotSubstitutions,
	estimateFDR,
	exportClusters,
	exportHighConfSub,
	exportCoverage,
	exportSequences
)



