Re: [MUMmer-help] show-diff documentation?

[Timothy Wu <2h...@gm...>]

Hi,

Could someone help me with this question I posted at BioStar?

Thanks.

https://www.biostars.org/p/130363/

Timothy



On Thu, Dec 11, 2014 at 3:24 PM, Timothy Wu <2h...@gm...> wrote:

> Dear Adam,
>
> Yes that was indeed me. That email account is not stable as of lately.
> I've been missing many emails from many people. Thanks for your help I
> appreciate it. That top-level README is easy to miss but definitely more
> descriptive.
>
> Everything else is clear, however, I am not sure about GAP.
>
> "gap-length-R is the length of the alignment gap in the reference". I
> don't understand when itself (or gap-legnth-Q for that matter) is negative,
> where gap_end - gap_start is negative. (Why is the coordinates for end
> smaller than start?) Hence I don't follow where it says "If gap-diff is
> positive, sequence has been inserted in the reference", and the rest of the
> explanations.
>
> GAP is suppose to be different from BRK or DUP, why is it talking about
> tandem duplications, and not label it as DUP? (BTW what does BRK stands
> for?)
>
> Thanks for your help. :)
>
> Timothy
>
>
>
> Timothy
>
>
> On Fri, Nov 21, 2014 at 12:45 AM, Adam Phillippy <aph...@gm...>
> wrote:
>
>> Timothy,
>> The documentation for show-diff is in the top-level README (in
>> MUMmer/README). I also believe I responded with additional information to
>> an email you sent directly to me yesterday. (or at least to someone who
>> happens to have your same name!)
>>
>> Best,
>> -Adam
>>
>>
>> On Wed, Nov 19, 2014 at 9:35 PM, Timothy Wu <2h...@gm...> wrote:
>>
>>> Hi,
>>>
>>> I would like to know if there is any documentation for show-diff. I find
>>> it difficult to understand. The documentation to dnadiff told us to see
>>> documentation for various tools, but I can't find any doc for show-diff.
>>> I've read the stuff with the -h flag but I still find it hard to digest.
>>> Any help appreciated, thanks.
>>>
>>> Timothy
>>>
>>>
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>>
>