Re: [Seqan-dev] SAM issue?

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

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>

--
Manuel Holtgrewe			manuel.holtgrewe@fu-berlin.de
Freie Universität Berlin		http://www.inf.fu-berlin.de/
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