[Seqan-dev] Gapped Sequence Itertor seems to trim Gaps at Beginning/Ending of a Row

[Nikola Koch <s9nikoch@stud.uni-saarland.de>]

Hi,
I'm using Seqan for my Bachelor's thesis, which consists of writing an  
alignment window for BALL.
Since I need to have pointers from the sequences back to the  
corresponding residues, I have to create my own sequence and alignment  
representations that link back to their origins.
For computing the actual alignment, I want to use Seqan.
So I have to push my representations into the Seqan structures and  
after computing the alignment, retrieve the alignment from the Seqan  
structures and push it into my own structures. The Seqan structures I  
use, are the same as described in your tutorial (I'm not using an  
alignment graph)
And here comes my problem:
When retrieving the Alignment from your structures I use two iterators  
to iterate over the gapped rows (and columns).
But when there are gaps at the beginning (or the end) of a row, the  
iterator seems to just ignore them and starts with the character right  
after the gap (or ends with the last character in front of the gap).
For example: ---AL-GI-- then becomes AL-GI.

The length of such a gapped row seems to also be the length of the row  
without starting/ending gaps.

But when using std::cout with the whole alignment, all gaps are, where  
they should be.

I consulted the Seqan documentation but without result.

So is there a possibility to externally gain access to the gaps at the  
beginning/end of each row?
Or is there a better way to retrieve the alignment than iterating over  
all rows?

Thanks,
Nikola