[BioC] CIGAR-aware coverage

[Hervé Pagès]

Hi Chris,

On 02/27/2014 11:00 PM, chris warth wrote:
>> 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?

It's not coverage() that cares. It's the internal coercion to
GRangesList that happens internally before the coverage is actually
computed. This internal coercion tries to propagate the metadata
columns, but, for reasons I never really understood, GRanges and
GRangesList objects are not allowed to hold a metadata column named
"strand". The fix is easy: this internal coercion to GRangesList should
not propagate the metadata columns (they're not needed for computing the
coverage and they slow down the coercion). I'll fix this today.

Thanks for the report.
H.

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-- 
Hervé Pagès

Program in Computational Biology
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