[Bioc-devel] GAlignments Constructor Type Checking Error
d@tr7320 @end|ng |rom un|@@ydney@edu@@u
Sun Apr 14 08:00:43 CEST 2019
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.
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)
factor-Rle of length 1 with 1 run
Values : +
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?
University of Sydney
Camperdown NSW 2050
More information about the Bioc-devel