open multiple BamWriters

[tlx...@gmail.com]

Hi everyone,

I want to split one bam file into several bam files and I am trying to use std::vector<BamTools::BamWriter> to open multiple BamWriters:

std::vector<BamTools::BamWriter> vBW(10);
for(int i=0;i<10;i++){
    if (!vBW[i].Open(filename[i], header, references)) {
        cerr << "Could not open output BAM file "<<filename[i] << endl;
        ......
    }
}

The source code can be compiled correctly but there is segmentation fault in this part while running. Anyone knows how to correctly open multiple BamWriters at the same time?

Best,

Lin

[Derek Barnett]

Hi Lin,
I've verified & reproduced the bug you mentioned. Thanks for the heads-up.

The current workaround for this is to use a pointer to your BamWriter:

std::vector<BamTools::BamWriter*> writers(numInput, 0);
for ( int i = 0; i < numInput; ++i ) {
  writers[i] = new BamWriter;
  if ( !writers[i]->Open(....) {
     cerr << .....
  }
}
// do stuff with writers, and then
// later on, cleanup
for ( int i = 0; i < numInput; ++i ) {
    if ( writers[i] ) {
       writers[i]->Close();
       delete writers[i];
       writers[i] = 0;
    }
}

I know it's a little extra effort to manage the memory manually, but it will work. In fact several command-line utilities (e.g. 'bamtools split', and API classes (e.g. BamMultiReader) use this approach for readers & writers. There are other reasons I had used the pointer approach, but that at least explains why I haven't seen this behavior so far. I'm sure it has to do with the pimpl not playing well with STL copy behavior for containers. I'll make a note to fix this in the next major release.

Please let me know this helps or not.
  - Derek

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[Lin Song]

Hi Derek,

I tried the pointer approach in my program and it works exactly as what I wish. Thank you very much! 

Best,

Lin

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