@@ -14,20 +14,24 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    output = file_path_sans_ext(input_a, TRUE),

                    consolidate = TRUE, ...)

           {

+            output_dir <- dirname(output)

+            if (!file.exists(output_dir))

+              dir.create(output_dir, recursive = TRUE)

+

             params <- initialize(params, ...)

             params_list <- as.list(params)

             if (gsnap_split_output(params)) {

               params_list$split_output <- output

+              output_path <- output_dir

             } else {

-              params_list$.redirect <- paste0("> ", output, ".sam")

+              output_path <- paste0("> ", output, ".sam")

+              params_list$.redirect <- output_path

             }

-            output_dir <- dirname(output)

-            if (!file.exists(output_dir))

-              dir.create(output_dir, recursive = TRUE)

             do.call(.gsnap, c(.input_a = input_a, .input_b = input_b,

                               format = "sam", params_list))

-            gsnap_output <- GsnapOutput(path = output_dir, version = gsnapVersion(),

+            gsnap_output <- GsnapOutput(path = output_path,

+                                        version = gsnapVersion(),

                                         param = params)

             asBam(gsnap_output)

             if (consolidate)

@@ -71,8 +75,8 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    sam_headers_batch = NULL, read_group_id = NULL,

                    read_group_name = NULL, version = FALSE,

                    .input_a = NULL, .input_b = NULL,

-                   .redirect = NULL, ## e.g., > gsnap.sam

-                   extra = NULL)

+                   .redirect = NULL ## e.g., > gsnap.sam

+                   )

 {

   formals <- formals(sys.function())

   problems <- do.call(c, lapply(names(formals), .valid_gmap_parameter, formals))

@@ -84,8 +88,6 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

   batch <- match.arg(batch)

   mode <- match.arg(mode)

   quality_protocol <- match.arg(quality_protocol)

-    

-  if (identical(extra, list())) extra <- NULL

 ### TODO: if input_a is NULL, or split_output and .redirect are NULL:

 ###       return a pipe()