Michael Lawrence authored on 20/11/2018 18:59:59
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@@ -10,7 +10,7 @@ |
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cmetindex <- function(db, use_snps = NULL) {
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if (!is(db, "GmapGenome")) |
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stop("'db' must be a GmapGenome object")
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- .cmetindex(genome(db), directory(db), directory(db), use_snps = use_snps) |
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+ .cmetindex(genome(db), directory(db), use_snps = use_snps) |
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} |
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 02/08/2012 22:24:24
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new file mode 100644 |
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@@ -0,0 +1,25 @@ |
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+### ========================================================================= |
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+### cmetindex command |
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+### ------------------------------------------------------------------------- |
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+### |
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+ |
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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+### High-level wrapper |
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+### |
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+ |
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+cmetindex <- function(db, use_snps = NULL) {
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+ if (!is(db, "GmapGenome")) |
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+ stop("'db' must be a GmapGenome object")
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+ .cmetindex(genome(db), directory(db), directory(db), use_snps = use_snps) |
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+} |
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+ |
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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+### Low-level wrapper |
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+### |
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+ |
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+.cmetindex <- function(db = "hg19", sourcedir = NULL, destdir = NULL, |
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+ use_snps = NULL) |
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+{
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+### TODO: assertions |
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+ .system(commandLine("cmetindex"))
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+} |