Re: [Seqan-dev] SAM issue?

[Mat <matthias.dodt@mdc-berlin.de>]

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>