@@ -8,7 +8,7 @@

 setClass("BamTallyParam",

          representation(genome = "GmapGenome",

-                        which = "GenomicRanges",

+                        which = "GenomicRanges_OR_GRangesList",

                         desired_read_group = "character_OR_NULL",

                         minimum_mapq = "integer",

                         concordant_only = "logical",

@@ -32,8 +32,8 @@ setClass("BamTallyParam",

 ###

 normArgWhich <- function(x, genome) {

-  if (!is(x, "GenomicRanges"))

-    stop("'which' must be a GenomicRanges")

+  if (!is(x, "GenomicRanges_OR_GRangesList"))

+    stop("'which' must be a GenomicRanges or GRangesList")

   si <- seqinfo(genome)

   seqinfo(x, new2old = match(seqlevels(si), seqlevels(x))) <-

     merge(si, seqinfo(x))