@@ -125,7 +125,7 @@ setMethod("consolidate", "GsnapOutput", function(x) {

 ##converts all gsnap SAM files to BAM files and creates the .bai index files

 setMethod("asBam", "GsnapOutput",

-          function(file, indexDestination=TRUE) {

+          function(file) {

             ## the input is not a file. It is a GsnapOutput,

             ## but param name is enforced

             gsp <- file 

@@ -134,7 +134,7 @@ setMethod("asBam", "GsnapOutput",

             ##output directory. Only take those produced by gsnap.

             samFiles <- samPaths(gsp)

             mapply(asBam, file = samFiles, dest = samFiles,

-                   overwrite = TRUE, indexDestination=indexDestination)

+                   overwrite = TRUE)

             unlink(samFiles)            

 })

@@ -12,7 +12,7 @@ setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)

 setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

           function(input_a, input_b, params,

                    output = file_path_sans_ext(input_a, TRUE),

-                   consolidate = TRUE, indexDestination=TRUE, ...)

+                   consolidate = TRUE, ...)

           {

             output_dir <- dirname(output)

             if (!file.exists(output_dir))

@@ -41,7 +41,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

             gsnap_output <- GsnapOutput(path = output_path,

                                         version = gsnapVersion(),

                                         param = params)

-            asBam(gsnap_output, indexDestination=indexDestination)

+            asBam(gsnap_output)

             if (consolidate)

               consolidate(gsnap_output)

             return(gsnap_output)