Sean and Ivan,
Thanks for the insight. I'll look at devising a compromise within the
existing framework. I need to explore the various methods for GRanges
object to better understand the impact of a compromise. We started with
the simplest interpretation of limit bounds because it simplifies the
code. For example, we need to establish the rules for coverage or
findOverlaps when the DNA is circular or the alignment runs off the end
of a linear chromosome.
Patrick
On 4/27/10 8:05 AM, Sean Davis wrote:
On Tue, Apr 27, 2010 at 10:51 AM, Ivan Gregoretti<[email protected]> wrote:
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.
I guess that I mean to say that the two issues of aligning off the end
of the chromosome and handling circular genomes are related but
separate issues. An override seems quite reasonable for dealing with
the former. Until aligners or common formats (BAM/SAM) deal with the
latter, it will be difficult to deal appropriately with circular
genomes, so an override is probably a fine compromise.
Sean
And yes indeed: aligners do align a little bit past the boundaries
even for linear chromosomes. Thanks for pointing that out!
Ivan
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