Good day,
Although the documentation states "Generally not used directly", I'm trying it.
A small example fails because the input is evaluated to be in the wrong format,
but it doesn't seem so when I look at the variable type of strand.
debug(GAlignments)
GAlignments("chr1", 1L, strand = Rle(factor('+')), cigar = "10M")
debug: new("GAlignments", NAMES = names, seqnames = seqnames,
start = pos, cigar = cigar, strand = strand, elementMetadata =
elementMetadata,
seqinfo = seqinfo)
Browse[2]> strand
factor-Rle of length 1 with 1 run
Lengths: 1
Values : +
Levels(1): +
Browse[2]> n
Error in validObject(.Object) :
invalid class “GAlignments” object: 'strand(x)' must be an unnamed 'factor'
Rle with no NAs (and with levels +, - and *)
This looks like a false-positive to me. Also, it would increase readability if
the constructor didn't run off the edge of the PDF page in the reference manual
by using \preformatted. Also, I wonder why seqnames is automatically converted
into a factor Rle, but strand isn't. Couldn't strand also use .asFactorRle?
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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