@@ -173,6 +173,18 @@ setClass("GsnapOutputList",

 setClass("SimpleGsnapOutputList",

          contains = c("GsnapOutputList", "SimpleList"))

+GsnapOutputList <- function(...) {

+  args <- list(...)

+  if (length(args) == 1 && is.list(args[[1]])) 

+    args <- args[[1]]

+  IRanges:::newList("SimpleGsnapOutputList", args)

+}

+

+setAs("GsnapOutputList", "BamFileList", function(from) {

+  BamFileList(lapply(from, as, "BamFile"))

+})

+

+

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

 ### Show

 ###

@@ -14,6 +14,15 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    output = file_path_sans_ext(input_a, TRUE),

                    consolidate = TRUE, ...)

           {

+            if (!is.null(input_b) && length(input_a) != length(input_b))

+              stop("If 'input_b' is non-NULL, it must have the same length",

+                   " as 'input_a'")

+            if (length(input_a) > 1L) {

+              return(GsnapOutputList(mapply(gsnap, input_a, input_b,

+                                            MoreArgs = list(params, output,

+                                              consolidate, ...))))

+            }

+            

             output_dir <- dirname(output)

             if (!file.exists(output_dir))

               dir.create(output_dir, recursive = TRUE)