@@ -154,21 +154,20 @@ GsnapParam <- function(genome, unique_only = FALSE,

                        split_output = !unique_only,

                        novelsplicing = FALSE, splicing = NULL, 

                        nthreads = 1L, part = NULL, batch = "2", ...) {

-  params <- formals(sys.function())

-  mc <- as.list(match.call(expand.dots = FALSE))[-1L]

-  params[names(mc)] <- mc

+  args <- formals(sys.function())

+  params <- mget(names(args), environment())

   params$unique_only <- NULL

+  paramClasses <- getSlots("GsnapParam")

+  paramClasses <- paramClasses[setdiff(names(paramClasses), c("extra", "snps"))]

+  params <- mapply(as, params[names(paramClasses)], paramClasses,

+                   SIMPLIFY = FALSE)

   if (!is.null(snps)) {

     if (!is(snps, "GmapSnps")) {

-      params$snps <- GmapSnps(snps, genome)

+      snps <- GmapSnps(snps, genome)

     }

+    params$snps <- snps

   }

-  dots <- list(...)

-  ##TODO: this breaks if ... has anything in it

-  if (length(dots) > 0) {

-    params$extra <- params$...

-  }

-  params$... <- NULL

+  params$extra <- list(...)

   do.call(new, c("GsnapParam", params))

 }

@@ -200,6 +199,18 @@ setAs("GsnapParam", "list", function(from) {

 setMethod("as.list", "GsnapParam", function(x) as(x, "list"))

+setAs("ANY", "characterORNULL", function(from) {

+  if (is.null(from))

+    NULL

+  else as.character(from)

+})

+setAs("ANY", "integerORNULL", function(from) {

+  if (is.null(from))

+    NULL

+  else as.integer(from)

+})

+

+

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