Re: [Denovoassembler-devel] RE : pull request for GenomeAssemblyReader

[Maxime D. <max...@gm...>]

On 02/17/2014 04:55 PM, Sébastien Boisvert wrote:
> 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.
>
>

please pull from

https://github.com/Zorino/ray.git
fixkmerlen

>> cheers,
>>
>> Maxime
>>
>>
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