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# RefMasker
Mask homologies in fasta reference sequences based on an user provided ranking (IN DEVELOPMENT)
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The order of references is CRITICAL if you want to perform a reference masking by the last reference masked by all the others then the penultimate masked by all others except the last and and so on until there is only one reference remaining

@brief **Wrapper for Blastn from NCBI Blast**
Please see the Blast+ user manual document for further details
[MANUAL](http://www.ncbi.nlm.nih.gov/books/NBK1762/)
Basically the top level function Blastn.align processes sequences as follow:

* If a blastn database is provided it will attempt to validate it by creating and MakeblastdbWrapper.ExistingDB object.
* If the validation fails of if no database was provided a new database will be created by using MakeblastdbWrapper.NewDB from a reference fasta file
* A instance of BlastnWrapper.Aligner is then created by passing the DB object as an argument.
* A list of fasta file (each can contains many sequences) is then submitted one by one to the balst database though  BlastnWrapper.Aligner
* For each query fasta a list of BlastHit objects containing informations for blast hits found will be returned
* Hit lists are combined into a single flat list and returned at the end of Blastn.align execution.

@copyright [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
@author Adrien Leger - 2014
* <adrien.leger@gmail.com>
* <adrien.leger@inserm.fr>
* <adrien.leger@univ-nantes.fr>
* [Github](https://github.com/a-slide)
* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)