@@ -21,5 +21,9 @@ snpindex <- function(name, genome, destdir = NULL,

 .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"))

 }

new file mode 100644

@@ -0,0 +1,25 @@

+### =========================================================================

+### snpindex command

+### -------------------------------------------------------------------------

+###

+

+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+### 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)

+{

+  .system(commandLine("snpindex"))

+}