useDynLib(rSFFreader)

import(ShortRead)
import(methods)
import(IRanges)
import(Biostrings)

exportClasses(
  SffHeader, SffReads, SffReadsQ
)

exportMethods(
  show, detail, header, names, "names<-", id, length, width, 
  adapterClip, qualityClip, customClip, rawClip, fullClip, clipMode,
  "adapterClip<-", "qualityClip<-", "customClip<-", "clipMode<-",
  "[", append, writeFasta, writeFastq, writePhredQual, writeFastaQual
)

export(
  availableClipModes, solveSffSEW, writePhredQual, SffReads, sread, quality,
  load454SampleData, loadIonSampleData,
  readSff, readSffGeometry, readSffHeader, SffReadsQ
)
