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 -285I 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 firstname.lastname@example.org Freie Universität Berlin http://www.inf.fu-berlin.de/ Institut für Informatik Phone: +49 30 838 75246 Takustraße 9 Algorithmic Bioinformatics 14195 Berlin Room 021