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let users pass a 'param' when building a GmapGenome from a FaFile

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110762 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 20/11/2015 12:24:09
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@@ -30,9 +30,10 @@ setMethod("gmap_build", c("RTLFile", "GmapGenome"), function(x, genome, ...) {
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   gmap_build(import(x), genome, ...)
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 })
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-setMethod("gmap_build", c("FaFile", "GmapGenome"), function(x, genome, ...) {
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-  gmap_build(getSeq(x), genome, ...)
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-})
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+setMethod("gmap_build", c("FaFile", "GmapGenome"),
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+          function(x, genome, param, ...) {
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+              gmap_build(getSeq(x, param), genome, ...)
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+          })
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 setMethod("gmap_build", c("DNAStringSet", "GmapGenome"),
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           function(x, genome, ...) {