[FIX] Fixing translocation VCF in mason_variator.

git-svn-id: http://svn.seqan.de/seqan/trunk@14444 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing SVLEN output to negative number for deletions in Mason.

git-svn-id: http://svn.seqan.de/seqan/trunk@14445 e6417c60-b987-48fd-844e-b20f0fcc1017
[FEATURE,TEST] add alignExtend submodule to extras

This Patch contains all necessary things for extending an existing Align object. The user will be exposed a function that he or she can pass an align object (e.g. of a seed) to, as well as certain parameters and this Align object will be extended.

Features:
* supports banded and non-banded extension
* supports xDrop or full DP
* supports arbitrary scoring schemes

Differences to bkehr's seed extension:
* uses SeqAn DP code, this means that on average more cell operations might be necessary, otoh it is correct in DP-terms and not heuristic
* can use affine gap costs
* needs no "re-alignment", returns score of new alignment
* correct xdrop-extension without "tail of mismatches" in the end
* no conclusive results on xdrop performance, since bkehr's code keeps the tail of mismatches at end of an extension and "trimming" is non-trivial (e.g. using localAlignment() to trim will result in good, but much shorter alignments)[1]
* will benefit from further improvements to DP-code, since it plugs right in

Possible future tasks:
* if the DP code has working "dynamic band" code, this algorithm would probably benefit greatly, making it more akin to a true xdrop


[1] in my application benchmarks this module was 0-20% slower than bkehr's implementation with consecutive localAlignment trimming, but produced up to 50% more alignments that passed e-Value test.




git-svn-id: http://svn.seqan.de/seqan/trunk@14446 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX,API] make const StringSets return const members

This patch defines the values in a const stringset to be const as well.
This behaviour is different to before, where you could have a const StringSet
of non-const Strings. The new behaviour is correct and intended according
weese and was required to make certain constructs like ReverseComplements
on members of ConcatDirect strings possible.

This patch was reviewed by weese. 



git-svn-id: http://svn.seqan.de/seqan/trunk@14447 e6417c60-b987-48fd-844e-b20f0fcc1017
[FEATURE,TEST] add translation module

This module includes code to do nucleaic acid translation to amino acid alphabet. The only things visible to the user are the translate function, an options enum and tags for the different translation tables. All currently used translation tables according to ncbi are included.
The implementation uses OpenMP if not disabled.

The code is fast :) Using OpenMP and ConcatDirect Sets for input and output it is possible to translate ~14million reads of ~100bp length in 2.3seconds on sequoia (excluding IO-time, including time for memory allocation of the target StringSet).




git-svn-id: http://svn.seqan.de/seqan/trunk@14448 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC,INTERNAL] minor changes code and doc

* fixed issues in doc and added more references
* moved a tiny check to happen at compile time instead of run-time



git-svn-id: http://svn.seqan.de/seqan/trunk@14449 e6417c60-b987-48fd-844e-b20f0fcc1017