Talk:General feature format

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Half-open versus closed[edit]

User:Jason.weirather's January 14th edit states that GFF's end coordinate has the same value as 0-based half-open formats' (e.g. BED's) end coordinate. This appears to have been intended as a restatement of the previous text, but it also adds the assumption that GFF represents intervals as closed. Citation needed; in particular, it seems to me that GMOD's GFF3 specification implies that GFF is half-open (emphasis added):

Columns 4 & 5: "start" and "end"

The start and end of the feature, in 1-based integer coordinates, relative to the landmark given in column 1. Start is always less than or equal to end.

For zero-length features, such as insertion sites, start equals end and the implied site is to the right of the indicated base in the direction of the landmark. These fields are required.

in which case GFF3's end coordinate would be one greater than BED's for the same feature.