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fix single output case for GMAP

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111240 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 05/12/2015 15:00:00
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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
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         methods to work with GMAP and GSNAP from within R. In addition,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.13.6
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+Version: 1.13.7
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12)
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 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),
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@@ -47,7 +47,7 @@ setMethod("gmap", c("character", "GmapParam"),
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                       output_path <- output_dir
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                   } else {
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                       output_path <- paste0(output, ".",
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-                                            formatToExt(params$format))
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+                                            formatToExt(params_list$format))
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                       params_list$.redirect <- paste(">", output_path)
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                   }
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