[Seqan-dev] Merging seeds

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

Hi,

I found that the seed merging depends on the order of the merge. For 
example:

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);bool 
yep = addSeed(seedset, Seed<int,SimpleSeed>(1, 1, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;
yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;

results in:
1 1 1-4
0 1 1-4

the seed containing a preceding location is not added.
On the other hand adding the seeds in reverse order, i.e.:

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);bool 
yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;
yep = addSeed(seedset, Seed<int,SimpleSeed>(1, 1, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;

gives what one expects:
1 1 0-3
1 1 0-4

Is this a feature or a bug? It should be annotated if it is the former.
It would also be nice to have an example for seed merging in demos 
(although I found some in tests).

Secondly, If I use the tag Single() while adding the second seed I get a 
compiler error:

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);
bool yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;
yep = addSeed(seedset, Seed<int,SimpleSeed>(1, 1, 4), 0, Single());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;

Thirdly, two adjacent seeds are currently not concatenated though it 
would make sense to join them I think:

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);
bool yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;
yep = addSeed(seedset, Seed<int,SimpleSeed>(4, 4, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;
  
gives:
1 1 0-3
0 1 0-3

rather than:
1 1 0-3
1 1 0-7

And finally, its called SeedSet but if a merge is not successful, like 
in the last example,  no new member  in the set is added (by default). 
Why so? Using appendValue() does also give a compiler error:

SeedSet< int, SimpleSeed,  DefaultNoScore , void > seedset(100, 0);
bool yep = addSeed(seedset, Seed<int,SimpleSeed>(0, 0, 4),Single());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;
yep = addSeed(seedset, Seed<int,SimpleSeed>(4, 4, 4), 0, Merge());
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;
if (not yep)
   appendValue(seedset, Seed<int,SimpleSeed>(4, 4, 4));
::std::cout << yep << " " << length(seedset) << " " << 
leftDim0(*begin(seedset)) << "-" << rightDim0(*begin(seedset)) << 
::std::endl;

Cheers,
Fabian

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