@@ -26,6 +26,8 @@ setClass("GsnapParam",

                         quiet_if_excessive = "logical",

                         nofails = "logical", 

                         split_output = "logical",

+                        terminal_threshold = "integer",

+                        gmap_mode = "character",

                         extra = "list"))

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

@@ -145,7 +147,7 @@ gsnap_extra <- function(x) {

 ### Constructor

 ###

-GsnapParam <- function(genome, unique_only = FALSE,

+GsnapParam <- function(genome, unique_only = FALSE, molecule = c("RNA", "DNA"),

                        max_mismatches = NULL,

                        suboptimal_levels = 0L, mode = "standard",

                        snps = NULL,

@@ -153,9 +155,12 @@ GsnapParam <- function(genome, unique_only = FALSE,

                        quiet_if_excessive = unique_only, nofails = unique_only,

                        split_output = !unique_only,

                        novelsplicing = FALSE, splicing = NULL, 

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

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

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

+                       gmap_mode = if (molecule == "DNA") "none", ...) {

   if (missing(genome))

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

+  molecule <- match.arg(molecule)

   args <- formals(sys.function())

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

   params$unique_only <- NULL