[Bioperl-guts-l] [Bug 2630] Bio::LocatableSeq range validation does not work with translated sequence coordinates

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Nov 16 01:07:04 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2630





------- Comment #3 from cjfields at bioperl.org  2008-11-16 01:07 EST -------
(In reply to comment #2)
> In order to allow frameshifts for HSPs I will be adding a frameshifts() method
> to LocatableSeq.  The data structure will likely be a simple internal hash with
> key = sequence positions of frameshifts and value = how many positions it is
> shifted relative to the sequence itself (1 or -1 for FASTA, but it could
> feasibly be more).  The end() calculation will start taking this into account
> when cross-checking passed end() args along with mapping criteria.

See bug 2663.


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