@@ -28,6 +28,7 @@ setClass("GsnapParam",

                         split_output = "logical",

                         terminal_threshold = "integer",

                         gmap_mode = "character",

+                        clip_overlaps = "logical",

                         extra = "list"))

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

@@ -158,7 +159,8 @@ GsnapParam <- function(genome, unique_only = FALSE, molecule = c("RNA", "DNA"),

                        nthreads = 1L, part = NULL, batch = "2",

                        terminal_threshold = if (molecule == "DNA") 1000L else 2L,

                        gmap_mode = if (molecule == "DNA") "none" else

-                       "pairsearch,terminal,improve", ...)

+                       "pairsearch,terminal,improve",

+                       clip_overlaps = FALSE, ...)

 {

   if (missing(genome))

     stop("The 'genome' must be specified (should be coercible to GmapGenome)")