PR 149

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PR 149

Roberto Alonso CIPF
Hello,

I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days ago, but I don't have any feedback yet, is there any problem with it? Is it not interesting for the current Galaxy? didn't the authors realized about it? It would be nice to have some feedback, even if it is not  a convenient PR.

Thanks so much,

Best regards


--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: [hidden email]

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Re: PR 149

John Chilton-4
No it just slipped through the cracks - sorry about that. I have
commented on it now. There was a time when a couple weeks before a
first response was the norm :).

Does it belong with the bam splitting pull request - is merging useful
on its own without the other piece you are working on.

-John




On Wed, Apr 29, 2015 at 11:04 AM, Roberto Alonso CIPF <[hidden email]> wrote:

> Hello,
>
> I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days
> ago, but I don't have any feedback yet, is there any problem with it? Is it
> not interesting for the current Galaxy? didn't the authors realized about
> it? It would be nice to have some feedback, even if it is not  a convenient
> PR.
>
> Thanks so much,
>
> Best regards
>
>
> --
> Roberto Alonso
> Functional Genomics Unit
> Bioinformatics and Genomics Department
> Prince Felipe Research Center (CIPF)
> C./Eduardo Primo Yúfera (Científic), nº 3
> (junto Oceanografico)
> 46012 Valencia, Spain
> Tel: +34 963289680 Ext. 1021
> Fax: +34 963289574
> E-Mail: [hidden email]
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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Re: PR 149

Roberto Alonso CIPF
Ok, no problems ;)
It is another PR, I think it is useful without the other PR, for example when you map with BWA. The last PR will be like the next step, I mean for example that  you split a bam to do some calling or whatever. I think both PR can live independently and together... I don't know if I self-explained well :)

Regards

On 29 April 2015 at 17:14, John Chilton <[hidden email]> wrote:
No it just slipped through the cracks - sorry about that. I have
commented on it now. There was a time when a couple weeks before a
first response was the norm :).

Does it belong with the bam splitting pull request - is merging useful
on its own without the other piece you are working on.

-John




On Wed, Apr 29, 2015 at 11:04 AM, Roberto Alonso CIPF <[hidden email]> wrote:
> Hello,
>
> I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days
> ago, but I don't have any feedback yet, is there any problem with it? Is it
> not interesting for the current Galaxy? didn't the authors realized about
> it? It would be nice to have some feedback, even if it is not  a convenient
> PR.
>
> Thanks so much,
>
> Best regards
>
>
> --
> Roberto Alonso
> Functional Genomics Unit
> Bioinformatics and Genomics Department
> Prince Felipe Research Center (CIPF)
> C./Eduardo Primo Yúfera (Científic), nº 3
> (junto Oceanografico)
> 46012 Valencia, Spain
> Tel: <a href="tel:%2B34%20963289680%20Ext.%201021" value="+34963289680">+34 963289680 Ext. 1021
> Fax: <a href="tel:%2B34%20963289574" value="+34963289574">+34 963289574
> E-Mail: [hidden email]
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/



--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: [hidden email]

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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Re: PR 149

Peter Cock
On Wed, Apr 29, 2015 at 4:40 PM, Roberto Alonso CIPF <[hidden email]> wrote:
> Ok, no problems ;)
> It is another PR, I think it is useful without the other PR, for example
> when you map with BWA. The last PR will be like the next step, I mean for
> example that  you split a bam to do some calling or whatever. I think both
> PR can live independently and together... I don't know if I self-explained
> well :)
>
> Regards

Logically splitting BAM files and merging BAM files are separate tasks,
and separate pull-requests make sense to me.

e.g.

Splitting FASTQ files for read mapping, then merging the BAM output.

Splitting BAM files for SNP calling, then merging the VCF output.

(Splitting BAM files is the more complex case, especially as often you
don't really want to touch the BAM file but rather split the processing
and exploit the BAI index - e.g. split a BED file of regions instead)

Peter
___________________________________________________________
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