Re: [Seqan-dev] SAM issue?

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

Another thing you could try is to read the SAM file, and write it out  
immediately after and see whether there are any problems with the  
generated SAM.

*m

Am 18.03.2011 um 17:05 schrieb Mat:

> Hi Manuel&thanks for the reply!
>
> I only send you the head of the SAM file i used- i don't get the  
> issue with that one either - so now i have to figure out what's  
> wrong there...
>
> Ill text you guys if i find an issue - thanks a lot!
>
> cheers
>
> mat
>
> Am 3/18/11 4:46 PM, schrieb Manuel Holtgrewe:
> > Hi, Mat.
> >
> > Here is what I get:
> >
> > $ ./demos/SAMtest -s bug.sam | grep -A 1 571
> > illumina_80bp_3kb.000000571
> > illumina_80bp_3kb.000000571
> > 19625,19705 and 22480,22400
> >
> > Which is OK since indices are 1-based in SAM and 0-based in SeqAn.
> >
> > I just saw that there were uninitialized variables in your code,  
> > try to compile it with all warnings enabled and in optimized mode  
> > (the compiler only detects certain things when you tell him to  
> > think harder about the code). Me getting the right values (probably  
> > my OS initializes data differently from yours), and you wrong  
> > indicates problems with initializations.
> >
> > Normally, I would also point you at valgrind, but it did not find  
> > the uninitialized memory on the stack :)
> >
> > Below is the C++ output:
> >
> > Building CXX object demos/CMakeFiles/SAMtest.dir/Users/manuel/ 
> > Development/seqan-trunk/projects/library/demos/SAMtest.cpp.o
> > /Users/manuel/Development/seqan-trunk/projects/library/demos/ 
> > SAMtest.cpp: In function ‘int main(int, const char**)’:
> > /Users/manuel/Development/seqan-trunk/projects/library/demos/ 
> > SAMtest.cpp:57: warning: ‘cId1’ may be used uninitialized in this  
> > function
> > /Users/manuel/Development/seqan-trunk/projects/library/demos/ 
> > SAMtest.cpp:57: warning: ‘id1’ may be used uninitialized in this  
> > function
> >
> >
> >
> > HTH
> >
> > Am 18.03.2011 um 15:52 schrieb Mat:
> >
> > > Hey guys!
> > >
> > > I have a strange issue loading a SAM-File into a FragmentStore.  
> > > The SAM file has the following paired-read alignment:
> > > ...
> > > illumina_80bp_3kb.000000571     99      contig00002     19626    
> > > 60      80M     =       22401   2855
> > > illumina_80bp_3kb.000000571     147     contig00002     22401    
> > > 60      80M     =       19626   -285
> > >
> > >
> > > I load this SAM file into a FragmentStore and sort it by  
> > > PairMatchId. Then i extract all the pairs that map on the same  
> > > contig:
> > >
> > > illumina_80bp_3kb.000000571
> > > illumina_80bp_3kb.000000571
> > > 19638,19718 and 22495,22415
> > >
> > > I don't really get why these coordinates differ?!
> > >
> > > Thanks a lot!!
> > >
> > > (see sourcecode attached)...
> > > <bug.sam><SAMtest.cpp><ATT00001..txt>
> <ATT00001..txt>

--
Manuel Holtgrewe			manuel.holtgrewe@fu-berlin.de
Freie Universität Berlin		http://www.inf.fu-berlin.de/
Institut für Informatik			Phone: +49 30 838 75246
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