[BioC] CIGAR-aware coverage

[chris warth]

> GenomicAlignments is mostly a reorganization of pre-existing functionality.
> You should be able to call coverage() directly on your GAlignments, or on
> the BamFile itself, with full support for cigar strings. Also, it is
> sufficient to call readGAlignments(), i.e., no need for "FromBam".
>

Thanks for this, I tried calling coverage() on GAlignments before and
it wouldn't work for me, but looking closer I now understand the
error.

 > class(myalignments)
 [1] "GAlignments"
 attr(,"package")
 [1] "GenomicRanges"

 > coverage(myalignments)
 Error in coverage(grglist(x, drop.D.ranges = drop.D.ranges), shift = shift,  :
  error in evaluating the argument 'x' in selecting a method for
function  'coverage': Error in validObject(.Object) :
  invalid class "GRangesList" object: 'mcols(x)' cannot have columns
named  "seqnames",  "ranges", "strand", "start", "end", "width",  or
"element"


Eliminating the metadata (what = c("pos", "qwidth", "strand")) in the
alignments allows coverage() to work now.

Why in the world does coverage() care if the alignments have strand metadata?