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

[Sébastien B. <seb...@ul...>]

I merged your changes.

I also added proper documentation (Ray -help )


Keep up the good work !!



On 17 février 2014 07:12, Maxime Déraspe [max...@gm...] wrote:
> À : Sébastien Boisvert; den...@li...
> Objet : Re: RE : [Denovoassembler-devel] pull request for GenomeAssemblyReader
> 
> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Managing the Performance of Cloud-Based Applications
>>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
>>> Read the Whitepaper.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Denovoassembler-devel mailing list
>>> Den...@li...
>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-devel
>