Re: [Seqan-dev] loading SeedSets cargos into maps

[Fabian Buske <f.buske@uq.edu.au>]

Hi,

I figured out a solution for the issue. Basically, the missing 
assignment operator (=) in several classes were causing the problem. I'm 
in the process of updating the related bug report in the bugtracker 
(which seems awfully slow by the way). I will attach all files modified 
by myself. I recommend a prompt merge with the current version of the 
library to avoid conflicts with subsequent file changes.

Thanks & cheers,
Fabian

Fabian Buske wrote:
> Hi,
>
> After not attracting any attention on this one I worked myself through 
> the MemoryManager, which seems to cause all the problems.
>
> First, the part the compiler complains about doesn't make any sense to 
> me at all. So I put the following lines in comments:
>
> memoryManager_int.h:
>
> //hmmmmmmmmmmm < this was not my comment; its not useful whatsoever
> size_t x = supremumValue<size_t>();
> while (tmpSource != x){
> tmpSource = source[tmpSource];
> target[tmpTarget] = tmpSource;
> tmpTarget = target[tmpTarget];
> }
>
> I also had to change a couple of lines above to prevent a bad memory 
> access. Changed:
>
> target.lastValue = &target[length(source)-1];
>
> to
> if (length(source) > 0) target.lastValue = &target[length(source)-1];
>
> I also have the other bugfixes that I did submit to the bug-tracker 
> (bug + fix) but unfortunately nobody has actually made the changes in 
> the library so far.
>
> *What I figured out:*
> The SeedSet is instantiated as a local variable and then added to the 
> map. That means everything is copied, at least it should, otherwise 
> its lost when the program leaves the scope of the SeedSet. However, 
> the memoryManager seems to recycle certain memory regions that contain 
> seeds. At least I loose the seed data when I leave the scope.
>
> TMap map;
> {
> TSeedSet seedset(100, 0);
> TSeed seed(1, 2, 4);
> if (!addSeed(seedset, seed, Single()))
> ::std::cerr << "adding seed went wrong" << ::std::endl;
> insert(map, 0, seedset); // insert the seedset at key=0
> printMap(map,-2,2); // Seeds still in map
> }
> printMap(map,-2,2); // Seeds gone from map
>
> Here, the second printMap() throws a memory access exception. The data 
> for the seed are lost:
>
> first printMap(map,-2,2):
> -2 missed
> -1 missed
> 0 found
> 1 1-4 2-5
> 1 missed
>
> second printMap(map,-2,2):
> -2 missed
> -1 missed
> 0 found
> Current language: auto; currently c++
> Program received signal: “EXC_BAD_ACCESS”.
>
> Any idea on how to fix this is very much appreciated since this bug 
> proves himself a stopper.
>
> Thanks a lot!
>
> Cheers,
> Fabian
>
> Fabian Buske wrote:
> > Hi,
> >
> > I tried to use a map (skiplist) loaded with an __int64 key and a 
> > seedSet cargo but get a compiler error.
> > Is there a size limit as to what load of a cargo or what type of 
> > cargo can be used?
> >
> > Sample code:
> >
> > typedef SeedSet< int, SimpleSeed, DefaultNoScore , void > TSeedSet;
> > typedef Pair< int, TSeedSet> TSkipValue;
> > typedef Map< TSkipValue , Skiplist< > > TDiagMap;
> > SeedSet< int, SimpleSeed, DefaultNoScore , void > seedset(100, 0);
> > TDiagMap diagMap;
> > insert(diagMap, 1, seedset);
> >
> > throws:
> >
> > seqan/seeds/memoryManager_int.h:185: error: cannot convert 'const 
> > seqan::Seed<int, const seqan::Tag<seqan::_Seed_simple> >' to 'size_t' 
> > in assignment
> > seqan/seeds/memoryManager_int.h:185: error: cannot convert 'const 
> > seqan::Seed<int, const seqan::Tag<seqan::_Seed_simple> >' to 'size_t' 
> > in assignment
> > seqan/seeds/memoryManager_int.h:185: error: cannot convert 'const 
> > seqan::Seed<int, const seqan::Tag<seqan::_Seed_simple> >' to 'size_t' 
> > in assignment
> >
> > I did put in a ticket for this as well.
> >
> > On a minor note seed_base and the seedSet_base are missing the "= 
> > operator" implementation.
> >
> > Seed & operator = (Seed const &orig)
> >
> >
> > Cheers,
> > Fabian
>
>
> --
> Fabian Buske
> Institute for Molecular Bioscience
> The University of Queensland 
> Brisbane, Qld. 4072 Australia
> Phone: (61)-(7)-334-62608
>   


--
Fabian Buske
Institute for Molecular Bioscience
The University of Queensland 
Brisbane, Qld. 4072 Australia
Phone: (61)-(7)-334-62608