Hi All,
Sorry for possible spam, but I am trying to customize IRanges package
locally. For what I am doing, I introduced another option to type
parameters to the findOverlaps method. In the file findOverlaps-methods.R,
I modified every instance of
type = c("any", "start", "end", "within", "equal"),
into
type = c("any", "start", "end", "within", "equal", "o"),

But when I call
h = findOverlaps(varanges, rna_tree, type="o")

I got the error
> h = findOverlaps(varanges, rna_tree, type="o")
Error in match.arg(type) :
  'arg' should be one of "any", "start", "end", "within", "equal"
with the following traceback information
> traceback()
5: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices),
       collapse = ", ")), domain = NA)
4: match.arg(type)
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(varanges, rna_tree, type = "o")
1: findOverlaps(varanges, rna_tree, type = "o")

Is there any place that I missed where there is a default type vector
specification?
Also, how do you guys get R to display filename and line numbers for the
methods in the traceback stack?

Best,
Yuan

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