[Seqan-dev] memory issue when calling function in seqan

[Lingjie Weng <wengl@uci.edu>]

Dear Seqan team,

I am interested in our Seqan C++ library, it is really helpful. But I 
got some problem when try to use the function 
"globalAlignment(Align<TSource, TSpec> & align_,Score<TScoreValue, 
Simple> const &, MyersBitVector" in seqan/align/align.myers.h file.

I was trying to call this function in my project, I called it in this 
way (got those code from /demos/alignment.cpp) :

    typedef String<Dna> TSequence;
    TSequence seq1 = "atcgaatgcgga";
    TSequence seq2 = "actcgttgca";
    Score<int> score(0, -1, -1, -2);
    Align<TSequence, ArrayGaps> align;
    resize(rows(align), 2);
    assignSource(row(align, 0), seq1);
    assignSource(row(align, 1), seq2);
    ::std::cout << "Score = " << globalAlignment(align, score, 
MyersBitVector()) << ::std::endl;

I found you have internally clean up the memory in the function 
"globalAlignment ()". My question is how could clean up the memory I 
allocated for initialization, for example, Tsequence, align...

When I am using it for millions  of reads alignment, the memory keeps 
increasing, which turns out to be a big issue to me. Do you have any 
idea how to release memory properly? I really appreciate if you could 
show me how to fix it.

I am looking forward to your reply.


Thanks,
Lingjie

PhD student
University of California, Irvine