\title{Build Gmap/Gsnap Genome}
  Construct the IIT (interval index tree) needed from the GMAP suite of tools to run from a
  genome file. IIT files are an oligomer index and what allow GMAP and GSNAP to
  efficiently lookup interval information for fast genomic
  mapping. \href{http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract}{Fast
    and SNP-tolerant detection of complex variants and splicing in short
    reads} offers an depth explication of IIT files and their use in GMAP and GSNAP. 

\item{\code{signature(x = "ANY", genome = "GmapGenome")}}{
%%  ~~describe this method here~~

\item{\code{signature(x = "character", genome = "GmapGenome")}}{
%%  ~~describe this method here~~

\item{\code{signature(x = "DNAStringSet", genome = "GmapGenome")}}{
%%  ~~describe this method here~~
\keyword{ ~~ other possible keyword(s) ~~ }

\item{d}{genome name}
\item{D}{destination directory for installation (defaults to gmapdb directory specified at configure time}
\item{k}{k-mer value for genomic index (allowed: 12..15, default 14)}
\item{S}{do not order chromosomes in numeric/alphabetic order, but use order in FASTA file(s)}
\item{g}{files are gzipped, so need to gunzip each file first}

\dontrun{flyGG <- GmapGenome(genome = "dm3",
                    directory = ggd)
gmap_build(x=Dmelanogaster, genome=flyGG)