R/atoiindex-command.R

In gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite

### =========================================================================
### atoiindex program
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###

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### High-level wrapper
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atoiindex <- function(db, use_snps = NULL) {
  if (!is(db, "GmapGenome"))
    stop("'db' must be a GmapGenome object")
  .atoiindex(genome(db), directory(db), directory(db), use_snps = use_snps)
}

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### Low-level wrapper
###

.atoiindex <- function(db = "hg19", sourcedir = NULL, destdir = NULL,
                       use_snps = NULL)
{
### TODO: assertions
  .system(commandLine("atoiindex"))
}