Re: [MUMmer-help] deltafilter -q (was: overlapping matches when calling mummer -mum)

[Afif E. <ael...@sd...>]

Hi, Adam,

On 11/03/2015 12:05 PM, Adam Phillippy wrote:
> Nucmer alignments will often overlap for the same reason MUMs can 
> overlap (repeats). In the example you give the alignments overlap on 
> the reference, but they do not overlap on the query. delta-filter -q 
> tries to find the best alignments that cover as much of the query 
> sequence as possible. Thus, this little 714 bp sequence appears 
> duplicated in your query, but not your reference. delta-filter keeps 
> it because it explains positions 3744105-3744818 on the query.

I understood that one, but I was referring to the middle line. Here is 
the snippet again:

3569553 3701911 3570622 *3702980* 132359  132359  99.99  4419977 
44259912.99    2.99 ...
3701734 3741905 *3702919* 3743090 40172   40172   99.98  4419977 
44259910.91    0.91 ...
3741192 3741905 3744105 3744818 714     714     98.60   4419977 
44259910.02    0.02 ...

The actual positions 3702919-3702980 in the query overlap in the first 
and second lines. I understand why the alignment is overlapping, but 
shouldn't delta-filter -q have filtered out the alignment corresponding 
to the second line here? In other words, is delta-filter -q /supposed/ 
to throw out all alignments that result in query overlaps?

>
> I promise you will find many similar examples as you continue to play 
> with the data. These types of alignments are very common when aligning 
> assemblies to references (due either to mis-assembly or true 
> variants), and sorting them all out is a very difficult problem.
>
Of course.

Many thanks and regards
Afif