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>
|
