@@ -24,8 +24,14 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

               params_list$split_output <- output

               output_path <- output_dir

             } else {

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

-              params_list$.redirect <- output_path

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

+              params_list$.redirect <- paste(">", output_path)

+            }

+

+            if (is.null(params_list$gunzip)) {

+              if (file_ext(input_a) == "gz" && file_ext(input_b) == "gz") {

+                params_list$gunzip <- TRUE

+              }

             }

             do.call(.gsnap,

@@ -65,7 +71,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

                    mode = c("standard", "cmet-stranded", "cmet-nonstranded",

                      "atoi-stranded", "atoi-nonstranded"),

                    tallydir = NULL, use_tally = NULL,

-                   use_runlength = NULL, nthreads = NULL,

+                   use_runlength = NULL, nthreads = 1L,

                    gmap_mode = "pairsearch,terminal,improve",

                    trigger_score_for_gmap = 5L, max_gmap_pairsearch = 3L,

                    max_gmap_improvement = 3L, microexon_spliceprob = 0.90,