@@ -15,6 +15,8 @@ setClass("GmapSnps",

 setGeneric("name", function(x) standardGeneric("name"))

+setMethod("name", "NULL", function(object) NULL)

+

 setMethod("name", "GmapSnps", function(x) {

   x@name

 })

@@ -182,15 +182,10 @@ setAs("GsnapParam", "list", function(from) {

   to$db <- genome(to$genome)

   to$dir <- path(directory(to$genome))

   to$genome <- NULL

-  if(!is.null(to$snps)) {

-    to$use_snps <- name(to$snps)

-  } else {

-    to$use_snps <- NULL

-  }

+  to$use_snps <- name(to$snps)

   to$snpsdir <- path(directory(to$snps))

-  to$snps <- NULL

   to$novelsplicing <- as.integer(to$novelsplicing)

-

+  to <- rename(to, splicing = "use_splicing")

   extras <- to$extra

   to <- c(to, extras)

   to$extra <- NULL