[Denovoassembler-devel] RE : pull request for GenomeAssemblyReader

[Sébastien B. <seb...@ul...>]

On 17 février 2014 06:36, Maxime Déraspe [max...@gm...] wrote:
> À : den...@li...
> Objet : [Denovoassembler-devel] pull request for GenomeAssemblyReader
> 
> Hi,
> 
> I have added 2 classes in Ray to load and "kmerized" any fasta files,
> it can be assembly contigs or reference genomes.
> 
> It aims to be used with Surveyor the same way as it was for loading a
> graph :
>     -read-sample-assembly
> instead of
>     -read-sample-graph
> 
> ------
> mpiexec -n 2 ../Ray \
>     -k 31 \
>     -output RaySurveyorResults-assembly \
>     -run-surveyor \
>     -read-sample-assembly test1 ./contigs/test.fasta \
>     -read-sample-assembly test2 ./contigs/test2.fasta \
> ------
> 
> it can be find in this commit
> bb7c62d5c8ed0dceab6571dcbac9382467b15de7
> @ https://github.com/Zorino/ray/commits/master
> 

Hi,


1. In Mother.cpp, why is there a +1 here:  actor->setKmerSize(m_parameters->getWordSize()+1);

2. +#define I_LIKE_FAST_IO n'est pas utilisé dans AssemblyReader.h


You should work in a branch.

When comment 1. is addressed, I'll merge. Comment 2. is not important.


> cheers,
> 
> Maxime
> 
> 
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