Re: [MUMmer-help] Show coords output last column

[Adam P. <aph...@gm...>]

Hi Nishadi,
I assume you are referring to the output with the -o commands? According to
the manual:

The -o annotations will appear in the final column of the output. The
descriptions reference the reference sequence, *e.g.* [END] means the
overlap is on the end of the reference sequence and [CONTAINED] means the
reference sequence is contained by the query sequence.

Looking at the code, it allows some wiggle for alignments that don't extend
to the very last base of a sequence, as long as it ends within a distance
<5% of the overlap length. It's not a very useful or flexible feature. If
you require a different definition of an overlap, it is easy to compute
directly from start/stop/length information in the other columns.

Best,
-Adam



On Wed, Jan 21, 2015 at 8:30 AM, Nishadi De Silva <nd...@sa...> wrote:

>  Hello
>
>  I am trying to work out how the last column in the show-coords output
> (e.g. IDENTITY, CONTAINED, CONTAINS) is determined but have failed to find
> any documentation on this online. I'd really be grateful if you could point
> me at some definitions as to how this information is deduced (in
> particular, how it deduces that one contig is contained in another).
>
>  Nishadi
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>
>
> ------------------------------------------------------------------------------
> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
> GigeNET is offering a free month of service with a new server in Ashburn.
> Choose from 2 high performing configs, both with 100TB of bandwidth.
> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
> http://p.sf.net/sfu/gigenet
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>