Re: [Gmod-ajax] setting up jbrowse with a bacterial reference genome

[Robert B. <rb...@gm...>]

Ah, I'd missed this up to now.  Yes, it seems it's all 0-based 
half-open.  I'll revert that commit.  Thanks a lot for pointing that out 
Karsten.

I'll add a ticket to convert everything shown to the user to be 1-based 
closed coordinates, because that's what people expect to see.

Rob

On 02/29/2012 05:21 PM, Karsten Hokamp wrote:
> Hi,
>
> I'm not sure this was a bug. In a previous discussion it was noted
> that JBrowse was 0-based, see from message 5 onwards in this thread:
> http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-td998491.html
>
> However, there was mentioning of changing this to 1-based for the user
> interface and I suppose this is done now.
>
> Thanks,
>
>      Karsten
>
>
> On Wed, Feb 29, 2012 at 8:06 PM, Robert Buels<rb...@gm...>  wrote:
>> Fixed in master, issue URL: https://github.com/gmod/jbrowse/issues/73
>>
>> On 02/28/2012 02:11 PM, Heewook Lee wrote:
>>> Done!
>>>
>>> On Tue, Feb 28, 2012 at 1:52 PM, Robert Buels<rb...@gm...
>>> <mailto:rb...@gm...>>  wrote:
>>>
>>>      Hi Heewook,
>>>
>>>      I'll take a look.  Could you add this to the JBrowse issue tracker at
>>>      https://github.com/GMOD/__jbrowse/issues
>>>      <https://github.com/GMOD/jbrowse/issues>?
>>>
>>>      Rob
>>>
>>>
>>>      On 02/27/2012 01:17 PM, Heewook Lee wrote:
>>>
>>>          I have noticed all entries in gff when it's added to jbrowse via
>>>          biodb-to-json.pl<http://biodb-to-json.pl>
>>>          <http://biodb-to-json.pl/>, start index  always
>>>
>>>          gets offset by 1. For example, if you have an entry in gff file and
>>>          start and end is 1000 2000, when it's added on jbrowse, it will
>>>          display
>>>          as "start: 999, end: 2000. Why does this happen and are you aware of
>>>          this? Thanks!
>>>
>>>
>>
>>
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