overlaps considers that Strand.FORWARD cannot overlap with Strand.INDEPENDENT #1650
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Hi @antonkulaga ! We have a The rationale for using |
@fnothaft I know about covers function as I use it actively in my projects. My question if we should change default extract behaviour to tolerate Strand.INDEPENDENT My practical experience with latest human and mouse genome releases tell me that we should (otherwise extract/extractRegions becomes useless in many cases as fragments there are always independent while features have direction) |
Hi @antonkulaga, check out #1513 & #1555. I think it resolves the issue of defaulting to |
I think this was resolved by #1637. |
Right now what I see that many reference genomes are imported with INDEPENDENT strand while in features we have FORWARD/REVERSE and functions like .extract fail to find features because FORWARD strand cannot overlap INDEPENDENT (overlaps functions uses sameStrand function that checks strand equality) and extract functions uses .overlaps inside of it. Maybe it makes sense to allow overlapping take place if the region that is being overlapped has INDEPENDENT strand?
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