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vectorize over 'output'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@129665 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 17/05/2017 20:11:24
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@@ -21,9 +21,10 @@ setMethod("gsnap", c("character", "character_OR_NULL", "GsnapParam"),
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             if (any(is.na(input_a)) || any(is.na(input_b)))
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               stop("'input_a' and 'input_b' must not contain NA's")
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             if (length(input_a) > 1L) {
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-              return(GsnapOutputList(mapply(gsnap, input_a, input_b,
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-                                            MoreArgs = list(params, output,
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-                                              consolidate, ...))))
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+                args <- list(params, consolidate, ...)
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+                return(GsnapOutputList(mapply(gsnap, input_a, input_b,
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+                                              output=output,
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+                                              MoreArgs = args)))
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             }
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             output_dir <- dirname(output)