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fix off-by-one error in bioperl flattener. fixes #73.
@skinner, that looks to me like some attempt to deal with UCSC coordinates. does something someplace else need to be fixed because of that?
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Whoa, the JBrowse code all assumes that coordinates are zero-based, half-open, like Chado. Which is The Right Way to do it (I'll follow up via email with the full essay for why that is). This is not an off-by-one error, this is exactly as intended. The way to fix #73 is for user-visible display messages to have code that does a " + 1" in them. That's the way UCSC does it; the code is all zero-based, half-open internally, and displays to users add one to the numbers.
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Yes, somebody already pointed that out on the gmod-ajax list, this was later reverted.
You don't have to write an essay on why that's the Right Way, I agree that interbase coordinates are the best internal representation.
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gmod-ajax thread was "setting up jbrowse with a bacterial reference genome"
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related issues are #73 and #74
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Ah, thanks, next time I'm catching up on my notifications I'll try and read everything before commenting.