git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@95333 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 11/10/2014 18:17:31
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@@ -50,7 +50,7 @@ setGeneric("genomeName", function(x) standardGeneric("genomeName"))
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setMethod("genomeName", "character", function(x) x)
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setMethod("genomeName", "BSgenome", function(x) providerVersion(x))
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-setMethod("genomeName", "FastaFile",
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+setMethod("genomeName", "RTLFile",
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function(x) file_path_sans_ext(basename(path(x)), TRUE)) |
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file_path_is_absolute <- function(x) {
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@@ -26,6 +26,10 @@ setMethod("gmap_build", c("FastaFile", "GmapGenome"), function(x, genome, ...) {
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gmap_build(path(x), genome, ...) |
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}) |
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+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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+ |
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setMethod("gmap_build", c("DNAStringSet", "GmapGenome"),
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function(x, genome, ...) {
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tmpfile <- tempfile() |