[BioC] CIGAR-aware coverage

Hervé Pagès hpages at fhcrc.org
Sat Mar 1 03:27:16 CET 2014

On 02/28/2014 09:47 AM, Hervé Pagès wrote:
> Hi Chris,
> On 02/27/2014 11:00 PM, chris warth wrote:
>> 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.

This is fixed in GenomicAlignments 0.99.27.


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