@@ -186,9 +186,9 @@ normArgTRUEorFALSE <- function(x) {

   x

 }

-normArgSingleCharacter <- function(x) {

+normArgSingleCharacterOrNULL <- function(x) {

   name <- deparse(substitute(x))

-  if (!is(x, "character") || length(x) != 1)

+  if (!is.null(x) && (!is(x, "character") || length(x) != 1))

     stop("'", name, "' should be a single character value")

   x

 }

@@ -206,7 +206,7 @@ normArgSingleCharacter <- function(x) {

                          indels = FALSE,

                          blocksize = 1000L, verbosep = FALSE,

                          include_soft_clips = 0L,

-                         cds_iit)

+                         exon_iit = NULL)

 {

   if (!is(bamreader, "GmapBamReader"))

     stop("'bamreader' must be a GmapBamReader")

@@ -245,7 +245,7 @@ normArgSingleCharacter <- function(x) {

         normArgSingleInteger(blocksize),

         normArgTRUEorFALSE(verbosep),

         normArgSingleInteger(include_soft_clips),

-        normArgSingleCharacter(cds_iit))

+        normArgSingleCharacterOrNULL(exon_iit))

 }

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -