I've been trying to work out why my fork is segfaulting on a string copy
(which suggests a memory overwrite error somewhere else), and found an
odd thing in the sequence loader (this is from sebhtml/ray:
void SequencesLoader::registerSequence(){
...
Read myRead;
myRead.constructor(read,&(*m_persistentAllocator),true);
m_myReads->push_back(&myRead);
...
}
note that the function returns void, but the address of a variable
declared in the function is stored in an array, with the expectation
that this address will be accessible later. I suspect that the memory
allocated for myRead will be flagged as available once the function
exits, causing problems (i.e. overwritten memory) later. I expect a fix
for this would go something like this:
void SequencesLoader::registerSequence(){
...
Read* myRead = new Read();
myRead.constructor(*read,&(*m_persistentAllocator),true);
m_myReads->push_back(myRead);
...
}
Note that the code will need to deallocate that memory later, once the
array of reads gets deleted.
There's also another (?related) issue in that Read doesn't have a
destructor, but it stores a uint8_t array which may need to be
deallocated (or somehow flagged for potential deallocation) once the
read structure is removed.
Unfortunately, changing the 'Read myRead' to a 'Read* myRead = new
Read()' doesn't fix my particular segfault problem, so I need to hunt
elsewhere. I assume that the problem is in code I've modified, because
I've done successful phiX assemblies with the current sebhtml/ray.
-- David
------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Denovoassembler-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
