[Seqan-dev] Using Fragment Store with soft-clipped alignments

[Pierre Pericard <pierre.pericard@lifl.fr>]

Dear SeqAn developers,

I'm currently working with SeqAn to read and compare alignments of NGS reads against reference sequences.

I found that the FragmentStore was a nice way to get what I need without too much code, which is what we're looking for in a library ;-)

However, depending on the aligner or the type of reads, I usually get a SAM with a large portion of soft-clipped alignments (especially with 454 reads), with CIGAR like this: 2S165M1D251M. And it seems that the FragmentStore is not able to handle soft-clipping in a SAM file...

Am I wrong ? As shown in "http://trac.seqan.de/wiki/Tutorial/FragmentStore/Assignment1", I would have expected to get a readGaps object already clipped according to the CIGAR in the SAM file. This should be possible using the setClippedBeginPosition() function of the Gaps class.
I was thinking about doing it manually once I had the readGaps object, but I couldn't find the CIGAR anywhere in the FragmentStore. Therefore, I'm stuck with read sequences incorrectly gapped because the alignment start position was not shifted.

Is there a way to go around the problem and still get a readGaps object soft-clipped as it should or do I need to give up using the FragmentStore ?

Thank you in advance for any idea.

Best regards.

Pierre Pericard

-- 
Pierre Pericard
PhD Student in Bioinformatics
Université Lille 1
BONSAI Team
http://www.lifl.fr/bonsai/

pierre.pericard@lifl.fr
Tel: +33 (0)3 28 77 85 60

LIFL, Bat M3
Cité scientifique
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FRANCE