@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods to work with GMAP and GSNAP from within R. In addition,

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

-Version: 1.13.6

+Version: 1.13.7

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.17.12)

 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),

@@ -47,7 +47,7 @@ setMethod("gmap", c("character", "GmapParam"),

                       output_path <- output_dir

                   } else {

                       output_path <- paste0(output, ".",

-                                            formatToExt(params$format))

+                                            formatToExt(params_list$format))

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

                   }