[Bioc-devel] GappedAlignments and AlignedRead should have a Seqinfo

[Martin Morgan]

On 02/18/2011 04:24 AM, Michael Lawrence wrote:
> Hi,
> 
> The GappedAlignments class is very useful, since we do not have to load the
> sequence information from a BAM file. I might suggest that GappedAlignments
> gain a Seqinfo slot (or an element in the metadata), which would be e.g.
> derived from the BAM header. That way, we get the right info on
> GRanges(List)s derived from the object and the coverage method can use the
> lengths. It would also be nice if AlignedRead could hold such information
> for when we care about the sequence.

Hi Michael -- I think there's a seqinfo slot in GappedAlignments
already, and that Rsamtools should just fill it in when
readBamGappedAlignments. I'll do that.

AlignedRead requires a bit more thought, in part because it doesn't
track metadata very well at all, and was in place before some of the key
infrastructure in IRanges was fully mature; this is on my radar...

Martin

> 
> Thanks,
> Michael
> 
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> 
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