### Compile the C code and load it automatically in R when loading the lib

useDynLib(Pasha, .registration = TRUE)


### Imports


# Bioconductor

import(IRanges)
import(GenomicAlignments)
import(Biostrings)
import(GenomicRanges)
import(Rsamtools)
import(ShortRead)
#import(GenomeInfoDb)


# General

importFrom(parallel, mclapply, mcmapply)
importFrom(bitops, bitAnd)
importFrom(tools, md5sum) # for functional tests
import(methods)
import(gtools) # mixedorder
import(S4Vectors) # Rle, metadata, metadata<-, runValue, runLength


# suggested by CRAN

importFrom("grDevices", "cairo_ps", "col2rgb", "dev.off", "pdf",
              "rainbow", "rgb", "svg")
importFrom("graphics", "abline", "axis", "barplot", "frame", "grid",
              "layout", "legend", "mtext", "par", "pie", "plot", "points",
              "polygon", "segments", "text")
importFrom("stats", "chisq.test", "density", "diffinv")
importFrom("utils", "packageVersion", "read.table", "untar")




### Exports

# Export all
exportClassPattern("^.*$")
exportPattern("^[^\\.C]")
