git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80186 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 10/09/2013 03:42:15
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@@ -27,7 +27,7 @@ setClass("GsnapParam",
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nofails = "logical", |
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split_output = "logical", |
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terminal_threshold = "integer", |
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- gmap_mode = "characterORNULL", |
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+ gmap_mode = "character", |
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extra = "list")) |
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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@@ -157,7 +157,9 @@ GsnapParam <- function(genome, unique_only = FALSE, molecule = c("RNA", "DNA"),
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novelsplicing = FALSE, splicing = NULL, |
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nthreads = 1L, part = NULL, batch = "2", |
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terminal_threshold = if (molecule == "DNA") 1000L else 2L, |
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- gmap_mode = if (molecule == "DNA") "none", ...) {
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+ gmap_mode = if (molecule == "DNA") "none" else |
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+ "pairsearch,terminal,improve", ...) |
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+{
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if (missing(genome)) |
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stop("The 'genome' must be specified (should be coercible to GmapGenome)")
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molecule <- match.arg(molecule) |