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region() behavior at the feature boundaries

See original GitHub issue

In my gff3, I have a feature that is seqid=x, start=a, end=b. By gff3 convention, both a and b are included. If I query for the single position a with region(seqid=x, start=a, end=a) I am not finding this feature, however if I query region(seqid=x, start=a, end=a+1) or region(seqid=x, start=a+1, end=a+1) I do find it. This seems inconsistent to me. Am I missing something? Is this behavior defined anywhere?

Issue Analytics

State:
Created 4 years ago
Reactions:1
Comments:9 (5 by maintainers)

Top GitHub Comments

1reaction

yl3commented, Jun 1, 2020

This issue seems to be caused by the fact that these lines in gffutils.FeatureDB.region() involve strict inequalities. The boundary base pairs get included correctly, if the lines are changed into

start_op = '<='
end_op = '>='

Could someone else check if this change is correct?

1reaction

littleblackfishcommented, May 22, 2020

This is exactly my experience. Thank you very much for characterizing the bug. I was working on something else by the time @daler replied and never got around to reproducing it.

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