### =========================================================================
 ### snpindex command
 ### -------------------------------------------------------------------------
 ###
 
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 ### High-level wrapper
 ###
 
 snpindex <- function(name, genome, destdir = NULL,
                      iitfile = paste(name, "iit", sep = "."))
 {
   .snpindex(sourcedir = path(directory(genome)), db = genome(genome),
             destdir = destdir, snpsdb = name, .iitfile = iitfile)
 }
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Low-level wrapper
 ###
 
 .snpindex <- function(sourcedir = NULL, db, destdir = NULL, snpsdb,
                       .iitfile = NULL)
 {

   if (is.null(destdir) && !file.exists(destdir)) {
     stop("The destination directory for the SNPs has not been created.",
          " Perhaps run GmapSnpDirectory with the \"create\" arg set to TRUE.")
   }

   .system(commandLine("snpindex"))
 }