git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@78423 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -26,6 +26,8 @@ setClass("GsnapParam", |
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quiet_if_excessive = "logical", |
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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 = "character", |
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extra = "list")) |
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|
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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@@ -145,7 +147,7 @@ gsnap_extra <- function(x) { |
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### Constructor |
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### |
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-GsnapParam <- function(genome, unique_only = FALSE, |
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+GsnapParam <- function(genome, unique_only = FALSE, molecule = c("RNA", "DNA"), |
|
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max_mismatches = NULL, |
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suboptimal_levels = 0L, mode = "standard", |
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snps = NULL, |
... | ... |
@@ -153,9 +155,12 @@ GsnapParam <- function(genome, unique_only = FALSE, |
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quiet_if_excessive = unique_only, nofails = unique_only, |
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split_output = !unique_only, |
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novelsplicing = FALSE, splicing = NULL, |
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- nthreads = 1L, part = NULL, batch = "2", ...) { |
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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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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) |
|
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args <- formals(sys.function()) |
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params <- mget(names(args), environment()) |
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params$unique_only <- NULL |