[Bioc-sig-seq] GRanges, failure assigning chromosome lengths

[Ivan Gregoretti]

Good morning Sean and everybody,

>
> Actually, the edge case is general as alignments, even on linear
> chromosomes, may extend beyond the end of the chromosome, I believe.
> In the best case, these alignments are clipped (in CIGAR terms), but I
> don't know that all aligners are doing that appropriately.
>
> Sean

So, you rather go for an overriding switch rather than infrastructure overhaul?

I ask this because GRanges is an exceptionally convenient format for
ChIP-seqers and Patrick is trying to make a decision to make it work
for real world data.

And yes indeed: aligners do align a little bit past the boundaries
even for linear chromosomes. Thanks for pointing that out!

Ivan