Re: [Seqan-dev] SAM issue?

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

It should: An insertion in the read regarding the reference inserts a gap which shifts all positions in the alignment right of it by one.

Am 21.03.2011 um 12:37 schrieb Mat:

> Ahh okay - well that might be a problem. But still i think the output shouldn't change with the number of lines in the sam file?!
> 
> thanks!
> 
> Am 3/21/11 12:14 PM, schrieb Holtgrewe, Manuel:
>> ontigStore                        TContigStore;
>> typedef typename Value<TContigStore>::Type                           TContig;
>> typedef typename TFragmentStore::TContigSeq                          TContigSeq;
>> typedef Gaps<TContigSeq, AnchorGaps<typename TContig::TGapAnchors> > TContigGaps;
>> 
>> typedef typename TFragmentStore::TAlignedReadStore                   TAlignedReadStore;
>> typedef typename Value<TAlignedReadStore>::Type                      TAlignedRead;
>> typedef typename TAlignedRead::TPos                                  TAlignedReadPos;
>> 
>> TContigGaps contigGaps(contigStore[contigId].seq, contigStore[contigId].gaps);
>> TAlignedRead const & alignedRead = alignedReadStore[idx];
>> // Translate end position from aligne
>> 
> <ATT00001..txt>