Empty sequence intervals

[Scott]

Hello Pygr folks,

Thanks for all the work on pygr, it's very useful tool.

I am curious why empty sequence intervals aren't allowed. One use
case of pygr is to model mutations (snp, insertions, deletions, etc).
When modeling an insertion it would be useful to treat it as an empty
sequence interval (hg19['chr7'][location:location] for example). I
have a work around in place that ignores the SeqPath bounds check.
This allows one to get the up and down stream flanking sequence for an
insertion. Is there a better way to model insertions with pygr?

Thanks,
Scott

[C. Titus Brown]

Hi Scott,

I think that's a good use case for empty sequence intervals, and one I
ran across myself a few months ago. I don't know if the NLMSA data
structure can handle this, however; Chris?

--titus
--
C. Titus Brown, c...@msu.edu