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Merge branch 'master' into whichAsGRangesList

Merge lawremi/gmapR into 'whichAsGRangesList'

alexandremkuhn authored on 31/08/2017 13:18:39
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@@ -21,7 +21,7 @@ setClass("GmapAlignerParam",
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                         extra = "list"))
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 setClass("GmapParam",
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-         representation(suboptimal_score = "integer",
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+         representation(suboptimal_score = "integer_OR_NULL",
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                         splicing = "logical",
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                         format = "character"),
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          contains="GmapAlignerParam")
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@@ -31,7 +31,7 @@ setClass("GmapParam",
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 ###
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 GmapParam <- function(genome, unique_only = FALSE,
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-                      suboptimal_score = 0L, mode = "standard",
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+                      suboptimal_score = NULL, mode = "standard",
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                       snps = NULL,
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                       npaths = if (unique_only) 1L else 100L,
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                       quiet_if_excessive = unique_only, nofails = unique_only,