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

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

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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