importFrom(Rsamtools, bamPaths, path)
importFrom(tools, list_files_with_exts)
importFrom(IRanges, isSingleString)

export(GsnapOutput)
exportClasses(GsnapOutput)
exportMethods(bamPaths, path)

export(buildGmapDbSNPIndex)
export(buildGmapIITFromFasta)
export(buildGmapIndex)
export(buildGsnapSNPIIT)
export(buildRefseqSpliceSites)
export(consolidateGmapFiles)
export(consolidateGsnapFiles)
export(exonsToGmapSpliceSites)
export(getGsnapFileCounts)
export(globals)
export(installGmap)
export(parallelized_gsnap)