[Bioperl-l] Bug? Features with similar ranges, different IDs are considered overlapping

Chris Fields cjfields at illinois.edu
Thu Aug 19 11:55:54 EDT 2010


On Aug 17, 2010, at 8:52 AM, Dave Messina wrote:

>> It seems to me that the genomic comparison is the thing people would do more often, so if you're going to create a flag, the default should be for the genomic comparison
> 
> Yep, agreed.
> 
> And such a flag should be named for the non-default behavior, then, like: -ignore_IDs_for_overlaps
> 
> Dave

Probably would just be -ignore_ids as this behavior would have to be consistent across the various Bio::RangeI methods (overlaps, contains, etc).  The params are case-insensitive IIRC, so the _IDs would just be lc().

RangeI doesn't define a seq_id(), though, so we either use can() in RangeI (which is dirtier IMO) or define this in the appropriate class, probably LocationI or SeqFeatureI.

chris



More information about the Bioperl-l mailing list