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

Fabian Buske <f.buske@uq.edu.au> · Tue, 22 Jun 2010 16:02:03 +1000

Dear Knut,

my apologies in case my comment came across the wrong way. I was not 

complaining about the bug fixing being slow but the actual process of 

submitting bugs/files to the bug tracker 

http://trac.mi.fu-berlin.de/seqan/, which takes a couple of minutes just 

for submitting  a tiny comment. At least from the other side of the 

world where I am sitting. However, I observe no time lag whatsoever when 

checking out from SVN.

Best regards,
Fabian

Reinert, Knut wrote:

Dear Fabian,

thank you very much for your reports and the bug fixes. Here in Germany we have the last 3 weeks of the Semester
and hence we are a bit bogged down and slow with fixing bugs.

All the best,

Knut Reinert

On Jun 22, 2010, at 3:51 AM, Fabian Buske wrote:

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

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--
Fabian Buske
Institute for Molecular Bioscience

The University of Queensland 

Brisbane, Qld. 4072 Australia

Phone: (61)-(7)-334-62608